Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses

Intrinsic disorder predictors were evaluated in several studies including the two large CAID experiments. However, these studies are biased towards eukaryotic proteins and focus primarily on the residue-level predictions. We provide first-of-its-kind assessment that comprehensively covers the taxonomy and evaluates predictions at the residue and disordered region levels. We curate a benchmark dataset that uniformly covers eukaryotic, archaeal, bacterial, and viral proteins. We find that predictive performance differs substantially across taxonomy, where viruses are predicted most accurately, followed by protists and higher eukaryotes, while bacterial and archaeal proteins suffer lower levels of accuracy. These trends are consistent across predictors. We also find that current tools, except for flDPnn, struggle with reproducing native distributions of the numbers and sizes of the disordered regions. Moreover, analysis of two variants of disorder predictions derived from the AlphaFold2 predicted structures reveals that they produce accurate residue-level propensities for archaea, bacteria and protists. However, they underperform for higher eukaryotes and generally struggle to accurately identify disordered regions. Our results motivate development of new predictors that target bacteria and archaea and which produce accurate results at both residue and region levels. We also stress the need to include the region-level assessments in future assessments.

Incidence and risk factors for catheter-associated urinary tract infection in 623 intensive care units throughout 37 Asian, African, Eastern European, Latin American, and Middle Eastern nations: A multinational prospective research of INICC

OBJECTIVE

To identify urinary catheter (UC)-associated urinary tract infection (CAUTI) incidence and risk factors.

DESIGN

A prospective cohort study.

SETTING

The study was conducted across 623 ICUs of 224 hospitals in 114 cities in 37 African, Asian, Eastern European, Latin American, and Middle Eastern countries.

PARTICIPANTS

The study included 169,036 patients, hospitalized for 1,166,593 patient days.

METHODS

Data collection took place from January 1, 2014, to February 12, 2022. We identified CAUTI rates per 1,000 UC days and UC device utilization (DU) ratios stratified by country, by ICU type, by facility ownership type, by World Bank country classification by income level, and by UC type. To estimate CAUTI risk factors, we analyzed 11 variables using multiple logistic regression.

RESULTS

Participant patients acquired 2,010 CAUTIs. The pooled CAUTI rate was 2.83 per 1,000 UC days. The highest CAUTI rate was associated with the use of suprapubic catheters (3.93 CAUTIs per 1,000 UC days); with patients hospitalized in Eastern Europe (14.03) and in Asia (6.28); with patients hospitalized in trauma (7.97), neurologic (6.28), and neurosurgical ICUs (4.95); with patients hospitalized in lower-middle-income countries (3.05); and with patients in public hospitals (5.89).The following variables were independently associated with CAUTI: Age (adjusted odds ratio [aOR], 1.01; P < .0001), female sex (aOR, 1.39; P < .0001), length of stay (LOS) before CAUTI-acquisition (aOR, 1.05; P < .0001), UC DU ratio (aOR, 1.09; P < .0001), public facilities (aOR, 2.24; P < .0001), and neurologic ICUs (aOR, 11.49; P < .0001).

CONCLUSIONS

CAUTI rates are higher in patients with suprapubic catheters, in middle-income countries, in public hospitals, in trauma and neurologic ICUs, and in Eastern European and Asian facilities.Based on findings regarding risk factors for CAUTI, focus on reducing LOS and UC utilization is warranted, as well as implementing evidence-based CAUTI-prevention recommendations.

Emergence of Long-Range Angular Correlations in Low-Multiplicity Proton-Proton Collisions

This Letter presents the measurement of near-side associated per-trigger yields, denoted ridge yields, from the analysis of angular correlations of charged hadrons in proton-proton collisions at sqrt[s]=13  TeV. Long-range ridge yields are extracted for pairs of charged particles with a pseudorapidity difference of 1.4<|Δη|<1.8 and a transverse momentum of 1 Collapse

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First Measurement of the |t| Dependence of Incoherent J/ψ Photonuclear Production

The first measurement of the cross section for incoherent photonuclear production of J/ψ vector mesons as a function of the Mandelstam |t| variable is presented. The measurement was carried out with the ALICE detector at midrapidity, |y|<0.8, using ultraperipheral collisions of Pb nuclei at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV. This rapidity interval corresponds to a Bjorken-x range (0.3-1.4)×10^{-3}. Cross sections are given in five |t| intervals in the range 0.04<|t|<1  GeV^{2} and compared to the predictions by different models. Models that ignore quantum fluctuations of the gluon density in the colliding hadron predict a |t| dependence of the cross section much steeper than in data. The inclusion of such fluctuations in the same models provides a better description of the data.

The Use of CECT in the Diagnosis of Intestinal Obstruction: A Case of Difficult Diagnosis in a Strangulated Left Femoral Hernia

ABSTRACT

A femoral hernia is an uncommon and acquired hernia in the groin. Its incidence in adults is 2%-8% of all abdominal wall hernias, and it has a female-to-male ratio of 1.8:1. It is usually found in elderly patients and is associated with increased morbidity due to delays in diagnosis leading to a high incidence of incarceration and strangulation. Accurate preoperative diagnosis of femoral hernia is challenging, especially in obese patients in whom a small femoral hernia can be hidden under the groin fat. Unlike an inguinal hernia, it rarely reduces on its own and if asymptomatic and small, is often unnoticed by the elderly obese patient. Femoral hernia is often unsuspected and overlooked in males as it is predominant among females. Delay in diagnosis can lead to intestinal gangrene and high morbidity. We present a case of an incarcerated left femoral hernia in an elderly obese male who presented with acute intestinal obstruction. He was managed with resection of the gangrenous segment and double barrel ileostomy. Although uncommon in males, a femoral hernia has a high incidence of strangulation, and therefore should always be ruled out as a cause of acute intestinal obstruction in elderly patients. Therefore, never forget to examine the groin in case of intestinal obstruction.

Measurement of energy and directional distribution of neutron ambient dose equivalent for the 7Li(p,n)7Be reaction

Double differential neutron fluence distributions were measured in the 7Li(p,n)7Be reaction for proton beam energies 7, 9 and 12 MeV. Seven liquid scintillator based detectors were employed to measure neutron fluence distributions using the Time of Flight technique. Neutron ambient dose equivalents were determined from the measured fluence distribution using ICRP (International Commission on Radiological Protection) recommended fluence to dose equivalent conversion coefficients. Neutron dose equivalents were also measured using a conventional BF3 detector based REM counter. Ambient dose equivalent measured by the REM counter is found to be in agreement with that determined from the neutron fluence spectra within their uncertainties. Angular distributions of the ambient dose equivalents were also determined from the measured fluence distributions at different angles.

ψ(2S) Suppression in Pb-Pb Collisions at the LHC

The production of the ψ(2S) charmonium state was measured with ALICE in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV, in the dimuon decay channel. A significant signal was observed for the first time at LHC energies down to zero transverse momentum, at forward rapidity (2.5 Collapse

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HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins

Current predictors of DNA-binding residues (DBRs) from protein sequences belong to two distinct groups, those trained on binding annotations extracted from structured protein-DNA complexes (structure-trained) vs. intrinsically disordered proteins (disorder-trained). We complete the first empirical analysis of predictive performance across the structure- and disorder-annotated proteins for a representative collection of ten predictors. Majority of the structure-trained tools perform well on the structure-annotated proteins while doing relatively poorly on the disorder-annotated proteins, and vice versa. Several methods make accurate predictions for the structure-annotated proteins or the disorder-annotated proteins, but none performs highly accurately for both annotation types. Moreover, most predictors make excessive cross-predictions for the disorder-annotated proteins, where residues that interact with non-DNA ligand types are predicted as DBRs. Motivated by these results, we design, validate and deploy an innovative meta-model, hybridDBRpred, that uses deep transformer network to combine predictions generated by three best current predictors. HybridDBRpred provides accurate predictions and low levels of cross-predictions across the two annotation types, and is statistically more accurate than each of the ten tools and baseline meta-predictors that rely on averaging and logistic regression. We deploy hybridDBRpred as a convenient web server at http://biomine.cs.vcu.edu/servers/hybridDBRpred/ and provide the corresponding source code at https://github.com/jianzhang-xynu/hybridDBRpred.

DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.

An international prospective study of INICC analyzing the incidence and risk factors for catheter-associated urinary tract infections in 235 ICUs across 8 Asian Countries

BACKGROUND

Identify urinary catheter (UC)-associated urinary tract infections (CAUTI) incidence and risk factors (RF) in 235 ICUs in 8 Asian countries: India, Malaysia, Mongolia, Nepal, Pakistan, the Philippines, Thailand, and Vietnam.

METHODS

From January 1, 2014, to February 12, 2022, we conducted a prospective cohort study. To estimate CAUTI incidence, the number of UC days was the denominator, and CAUTI was the numerator. To estimate CAUTI RFs, we analyzed 11 variables using multiple logistic regression.

RESULTS

84,920 patients hospitalized for 499,272 patient days acquired 869 CAUTIs. The pooled CAUTI rate per 1,000 UC-days was 3.08; for those using suprapubic-catheters (4.11); indwelling-catheters (2.65); trauma-ICU (10.55), neurologic-ICU (7.17), neurosurgical-ICU (5.28); in lower-middle-income countries (3.05); in upper-middle-income countries (1.71); at public-hospitals (5.98), at private-hospitals (3.09), at teaching-hospitals (2.04). The following variables were identified as CAUTI RFs: Age (adjusted odds ratio [aOR] = 1.01; 95% CI = 1.01-1.02; P < .0001); female sex (aOR = 1.39; 95% CI = 1.21-1.59; P < .0001); using suprapubic-catheter (aOR = 4.72; 95% CI = 1.69-13.21; P < .0001); length of stay before CAUTI acquisition (aOR = 1.04; 95% CI = 1.04-1.05; P < .0001); UC and device utilization-ratio (aOR = 1.07; 95% CI = 1.01-1.13; P = .02); hospitalized at trauma-ICU (aOR = 14.12; 95% CI = 4.68-42.67; P < .0001), neurologic-ICU (aOR = 14.13; 95% CI = 6.63-30.11; P < .0001), neurosurgical-ICU (aOR = 13.79; 95% CI = 6.88-27.64; P < .0001); public-facilities (aOR = 3.23; 95% CI = 2.34-4.46; P < .0001).

DISCUSSION

CAUTI rate and risk are higher for older patients, women, hospitalized at trauma-ICU, neurologic-ICU, neurosurgical-ICU, and public facilities. All of them are unlikely to change.

CONCLUSIONS

It is suggested to focus on reducing the length of stay and the Urinary catheter device utilization ratio, avoiding suprapubic catheters, and implementing evidence-based CAUTI prevention recommendations.

Measurements of Groomed-Jet Substructure of Charm Jets Tagged by D^{0} Mesons in Proton-Proton Collisions at sqrt[s]=13 TeV

Understanding the role of parton mass and Casimir color factors in the quantum chromodynamics parton shower represents an important step in characterizing the emission properties of heavy quarks. Recent experimental advances in jet substructure techniques have provided the opportunity to isolate and characterize gluon emissions from heavy quarks. In this Letter, the first direct experimental constraint on the charm-quark splitting function is presented, obtained via the measurement of the groomed shared momentum fraction of the first splitting in charm jets, tagged by a reconstructed D^{0} meson. The measurement is made in proton-proton collisions at sqrt[s]=13  TeV, in the low jet transverse-momentum interval of 15≤p_{T}^{jet ch}<30  GeV/c where the emission properties are sensitive to parton mass effects. In addition, the opening angle of the first perturbative emission of the charm quark, as well as the number of perturbative emissions it undergoes, is reported. Comparisons to measurements of an inclusive-jet sample show a steeper splitting function for charm quarks compared with gluons and light quarks. Charm quarks also undergo fewer perturbative emissions in the parton shower, with a reduced probability of large-angle emissions.

Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD

To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers and enhancer-promoter interactions, we have developed an approach to segment and extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds to chromatin for minutes, decompacts chromatin structure and increases enhancer dynamics. We also uncovered a rare fast-diffusing state of enhancers and found that NuRD restricts the time spent in this state. Hi-C and Cut&Run experiments revealed that NuRD modulates enhancer-promoter interactions in active chromatin, allowing them to contact each other over longer distances. Furthermore, NuRD leads to a marked redistribution of CTCF and, in particular, cohesin. We propose that NuRD promotes a decondensed chromatin environment, where enhancers and promoters can contact each other over longer distances, and where the resetting of enhancer-promoter interactions brought about by the fast decondensed chromatin motions is reduced, leading to more stable, long-lived enhancer-promoter relationships.

CoMemMoRFPred: Sequence-based Prediction of MemMoRFs by Combining Predictors of Intrinsic Disorder, MoRFs and Disordered Lipid-binding Regions

Molecular recognition features (MoRFs) are a commonly occurring type of intrinsically disordered regions (IDRs) that undergo disorder-to-order transition upon binding to partner molecules. We focus on recently characterized and functionally important membrane-binding MoRFs (MemMoRFs). Motivated by the lack of computational tools that predict MemMoRFs, we use a dataset of experimentally annotated MemMoRFs to conceptualize, design, evaluate and release an accurate sequence-based predictor. We rely on state-of-the-art tools that predict residues that possess key characteristics of MemMoRFs, such as intrinsic disorder, disorder-to-order transition and lipid-binding. We identify and combine results from three tools that include flDPnn for the disorder prediction, DisoLipPred for the prediction of disordered lipid-binding regions, and MoRFCHiBiLight for the prediction of disorder-to-order transitioning protein binding regions. Our empirical analysis demonstrates that combining results produced by these three methods generates accurate predictions of MemMoRFs. We also show that use of a smoothing operator produces predictions that closely mimic the number and sizes of the native MemMoRF regions. The resulting CoMemMoRFPred method is available as an easy-to-use webserver at http://biomine.cs.vcu.edu/servers/CoMemMoRFPred. This tool will aid future studies of MemMoRFs in the context of exploring their abundance, cellular functions, and roles in pathologic phenomena.

Non-Canonical p16-SP1 Signaling in Head and Neck Cancer Potentially Affects Cell Plasticity

PURPOSE/OBJECTIVE(S)

We have previously identified a non-canonical role for p16 in head and neck cancer (HNSCC) to repress homologous recombination (HR) via activation of a ubiquitin-mediated pathway. This was potentially via interaction with the transcription factor Sp1, however this interaction, as well as its downstream effects remain to be determined.

MATERIALS/METHODS

HPV- HN5 cells forced to overexpress p16 and HPV+ UM-SCC-47 cells p16 CRISPR knockout or shRNA to Sp1 were used. Following modulation, cells were evaluated via clonogenic assay and RNA Sequencing. Additionally, a nude mouse flank model of tumors derived from UM-SCC-47 cells expressing either scrambled control or Sp1 shRNA was performed to evaluate effects on tumor growth (n = 7/group).

RESULTS

Clonogenic assay revealed that, as expected, forced expression of p16 in HPV- cells significantly increased radiosensitivity, while CRISPR KO of p16 in HPV+ cells led to radioresistance. Preliminary results indicate a similar pattern observed when Sp1 is inhibited via shRNA. RNASeq data were examined to identify genes likely regulated by p16. Specifically, genes that were significant between p16 modulated cells (either forced expression or CRISPR KO; False Discovery Rate (FDR 1%)) with differences in expression tracking p16 (at least 1.5x higher in cells with intact p16) were evaluated via Ingenuity Pathway Analysis (IPA), with the most significant pathways repressed by p16 including: Stem cell signaling (p = 5e-4), Regulation of EMT (p = 9e-4) and WNT pathways (p = 1.6e-3). Initial results from in vivo studies indicate minimal, non-significant inhibitory effects on tumor growth following inhibition of Sp1 in UM-SCC-47. Confirmatory and radiation experiments are ongoing.

CONCLUSION

Our results indicate that non-canonical functions of p16 may extend beyond direct effects on HR to modulation of aspects of cell differentiation and plasticity. If accurate, p16 may be repressing EMT, contributing to its effects on radiosensitization.

Measurement of the Lifetime and Λ Separation Energy of _{Λ}^{3}H

The most precise measurements to date of the _{Λ}^{3}H lifetime τ and Λ separation energy B_{Λ} are obtained using the data sample of Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV collected by ALICE at the LHC. The _{Λ}^{3}H is reconstructed via its charged two-body mesonic decay channel (_{Λ}^{3}H→^{3}He+π^{-} and the charge-conjugate process). The measured values τ=[253±11(stat)±6(syst)]  ps and B_{Λ}=[102±63(stat)±67(syst)]  keV are compatible with predictions from effective field theories and confirm that the _{Λ}^{3}H structure is consistent with a weakly bound system.

Measurement of the J/ψ Polarization with Respect to the Event Plane in Pb-Pb Collisions at the LHC

We study the polarization of inclusive J/ψ produced in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV at the LHC in the dimuon channel, via the measurement of the angular distribution of its decay products. We perform the study in the rapidity region 2.5 Collapse

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First Measurement of Antideuteron Number Fluctuations at Energies Available at the Large Hadron Collider

The first measurement of event-by-event antideuteron number fluctuations in high energy heavy-ion collisions is presented. The measurements are carried out at midrapidity (|η|<0.8) as a function of collision centrality in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV using the ALICE detector. A significant negative correlation between the produced antiprotons and antideuterons is observed in all collision centralities. The results are compared with a state-of-the-art coalescence calculation. While it describes the ratio of higher order cumulants of the antideuteron multiplicity distribution, it fails to describe quantitatively the magnitude of the correlation between antiproton and antideuteron production. On the other hand, thermal-statistical model calculations describe all the measured observables within uncertainties only for correlation volumes that are different with respect to those describing proton yields and a similar measurement of net-proton number fluctuations.

Enhanced Deuteron Coalescence Probability in Jets

The transverse-momentum (p_{T}) spectra and coalescence parameters B_{2} of (anti)deuterons are measured in p-p collisions at sqrt[s]=13  TeV for the first time in and out of jets. In this measurement, the direction of the leading particle with the highest p_{T} in the event (p_{T}^{lead}>5  GeV/c) is used as an approximation for the jet axis. The event is consequently divided into three azimuthal regions, and the jet signal is obtained as the difference between the toward region, that contains jet fragmentation products in addition to the underlying event (UE), and the transverse region, which is dominated by the UE. The coalescence parameter in the jet is found to be approximately a factor of 10 larger than that in the underlying event. This experimental observation is consistent with the coalescence picture and can be attributed to the smaller average phase-space distance between nucleons in the jet cone as compared with the underlying event. The results presented in this Letter are compared to predictions from a simple nucleon coalescence model, where the phase-space distributions of nucleons are generated using pythia8 with the Monash 2013 tuning, and to predictions from a deuteron production model based on ordinary nuclear reactions with parametrized energy-dependent cross sections tuned on data. The latter model is implemented in pythia8.3. Both models reproduce the observed large difference between in-jet and out-of-jet coalescence parameters, although the almost flat trend of the B_{2}^{Jet} is not reproduced by the models, which instead give a decreasing trend.

Treatment Outcome with High versus low-to-moderate Dosing of Corticosteroids in Early vis-a-vis Late-onset Hypoxic Cases of COVID-19: A Multicentric Retrospective Cohort Study

Background

Corticosteroid dosing in COVID-19 cases associated with early-onset and late-onset hypoxia have not been separately explored.

Methods

In this retrospective cohort study, we divided hypoxic COVID-19 cases into groups based on timing of initiation of corticosteroids relative to onset of symptoms; Group A (≤6th day), Group B (7th-9th day) and Group C (≥10th day), each group being sub-grouped into high and low-to-moderate dose corticosteroid recipients. Cox regression with propensity scoring was used to compare 28-day mortality between high and low-to-moderate dose recipients separately in Group A, Group B, Group C.

Results

Among 505 patients included, propensity score matched Cox regression showed greater risk of all-cause mortality among high dose recipients in Group A [HR= 7.35, 95%CI 3.36-16.11, p-value<0·01, N=114] and Group B [HR=3.17, 95%CI 1.65-6.07, p-value<0·01, N=251]. In Group C, mortality was lowest [12.8% (18/140)] with no significant difference between sub-groups [HR=2.52, 95%CI 0.22-29.15, p-value=0.459, N=140]. Kruskal-Wallis Test between Group A, Group B and Group C for six pre-defined exposure variables showed significant differences for Neutrophil:Lymphocyte Ratio (NLR).

Conclusion

When steroids were initiated early (owing to an earlier onset of hypoxic symptoms), a high dose of corticosteroid was associated with greater overall 28-day mortality compared to a low-to-moderate dose. NLR, a marker for individual immune response, varied between treatment groups.

DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction

Intrinsic disorder in proteins is relatively abundant in nature and essential for a broad spectrum of cellular functions. While disorder can be accurately predicted from protein sequences, as it was empirically demonstrated in recent community-organized assessments, it is rather challenging to collect and compile a comprehensive prediction that covers multiple disorder functions. To this end, we introduce the DEPICTER2 (DisorderEd PredictIon CenTER) webserver that offers convenient access to a curated collection of fast and accurate disorder and disorder function predictors. This server includes a state-of-the-art disorder predictor, flDPnn, and five modern methods that cover all currently predictable disorder functions: disordered linkers and protein, peptide, DNA, RNA and lipid binding. DEPICTER2 allows selection of any combination of the six methods, batch predictions of up to 25 proteins per request and provides interactive visualization of the resulting predictions. The webserver is freely available at http://biomine.cs.vcu.edu/servers/DEPICTER2/.

Real-time Observation of Macroscopic Helical Morphologies under Optical Microscope: A Curious Case of π-π Stacking Driven Molecular Self-assembly of an Organic Gelator Devoid of Hydrogen Bonding

Supramolecular assemblies such as tubules/helix/double helix/helical tape etc. are usually submicron objects preventing direct observation under optical microscope. Chiral-pure form of these assemblies is important for potential applications. Herein, we report a rare phenomenon wherein a DMSO gel of a simple terpyridine derivative [(4-CNPhe)4PyTerp] produced macroscopic helical morphologies (μm length scale) which could be observed under optical microscope, formation of which could be monitored by optical videography, stable enough to withstand acidic vapour, robust enough to display reversible gel↔sol in response to acidic and ammonia vapour and sturdy enough to be maneuvered with a needle. These properties appeared to be unique to the title compound as the other related derivatives failed to display such assembly structures. SXRD and MD simulation studies suggested that weak interactions (π-π stacking) played a crucial role in the self-assembly process.

qNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids

Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since they must predict every amino acid in the input sequence and rely on multiple sequence alignments. We propose an alternative approach that predicts content (fraction) of the NA-binding residues, offering more information than the protein-level prediction and much shorter runtime than the residue-level tools. Our first-of-its-kind content predictor, qNABpredict, relies on a small, rationally designed and fast-to-compute feature set that represents relevant characteristics extracted from the input sequence and a well-parametrized support vector regression model. We provide two versions of qNABpredict, a taxonomy-agnostic model that can be used for proteins of unknown taxonomic origin and more accurate taxonomy-aware models that are tailored to specific taxonomic kingdoms: archaea, bacteria, eukaryota, and viruses. Empirical tests on a low-similarity test dataset show that qNABpredict is 100 times faster and generates statistically more accurate content predictions when compared to the content extracted from results produced by the residue-level predictors. We also show that qNABpredict's content predictions can be used to improve results generated by the residue-level predictors. We release qNABpredict as a convenient webserver and source code at http://biomine.cs.vcu.edu/servers/qNABpredict/. This new tool should be particularly useful to predict details of protein-NA interactions for large protein families and proteomes.

A rare case of abdominal cocoon associated with internal hernia in an adult

A transmesenteric internal hernia (TIH) is a protrusion of a viscus through the mesenteric defect. It is secondary to previous gastrointestinal surgery in an adult. Early diagnosis and management are warranted to prevent the strangulation of the bowel in a TIH. Here, we are reporting a case of a 24-year-old gentleman with COVID-positive status who has presented with cough, abdominal cocoon, and features of subacute intestinal obstruction (SAIO) without any previous history of abdominal surgery. A nonoperative trial is given in the management of abdominal cocoon with SAIO. In contrast, delay in surgical intervention in TIH leads to bowel gangrene. Surprisingly even on contrast-enhanced computed tomography of the abdomen, TIH was not picked up. We have diagnosed this case intraoperatively with gangrene of the bowel. In an abdominal cocoon without any history suggestive of tuberculosis or previous surgery, or any other condition that leads to an intra-abdominal reaction, an internal hernia should be kept as a differential diagnosis. The delay in diagnosis and surgical intervention is associated with potentially disastrous complications.

Severe acute pancreatitis in the early postoperative period due to afferent loop syndrome following gastrectomy for gastric cancer

Afferent loop syndrome (ALS) is an uncommon complication of gastrojejunostomy. It may be acute or chronic depending on whether symptoms manifest within 7 days of surgery. Rarely acute ALS may give rise to acute pancreatitis. It may present early in the postoperative course and, if diagnosed late, may result in organ failure within 48h. We report a middle-aged woman with carcinoma of the stomach managed by subtotal gastrectomy with Billroth II gastrojejunostomy and Braun jejunojejunostomy. The patient developed vomiting and abdominal pain in the first postoperative day with acute renal shutdown and about 500ml drain output of dirty fluid. On investigation, a diagnosis of acute pancreatitis due to afferent loop syndrome was made, and the patient was resuscitated in the intensive care unit. However, she showed early signs of organ failure and succumbed to her condition within 6 days of surgery. Since the complication is rare following gastrojejunostomy and often mimics ALS, an early diagnosis becomes difficult. If delay in management happens, premature organ failure may lead to high morbidity and mortality.

Comparison of suspected and confirmed internal EVD-related infections: a prospective multi-centre U.K. observational study

Background

Diagnosis of internal external ventricular drain (EVD)-related infections (iERI) is an area of diagnostic difficulty. Empiric treatment is often initiated on clinical suspicion. There is limited guidance around antimicrobial management of confirmed versus suspected iERI.

Methods

Data on patients requiring EVD insertion were collected from 21 neurosurgical units in the United Kingdom from 2014 to 2015. Confirmed iERI was defined as clinical suspicion of infection with positive cerebrospinal fluid (CSF) culture and/or Gram stain. Cerebrospinal fluid, blood, and clinical parameters and antimicrobial management were compared between the 2 groups. Mortality and Modified Rankin Scores were compared at 30 days post-EVD insertion.

Results

Internal EVD-related infection was suspected after 46 of 495 EVD insertions (9.3%), more common after an emergency insertion. Twenty-six of 46 were confirmed iERIs, mostly due to Staphylococci (16 of 26). When confirmed and suspected infections were compared, there were no differences in CSF white cell counts or glucose concentrations, nor peripheral blood white cell counts or C-reactive protein concentrations. The incidence of fever, meningism, and seizures was also similar, although altered consciousness was more common in people with confirmed iERI. Broad-spectrum antimicrobial usage was prevalent in both groups with no difference in median duration of therapy (10 days [interquartile range {IQR}, 7–24.5] for confirmed cases and 9.5 days [IQR, 5.75–14] for suspected, P = 0.3). Despite comparable baseline characteristics, suspected iERI was associated with lower mortality and better neurological outcomes.

Conclusions

Suspected iERI could represent sterile inflammation or lower bacterial load leading to false-negative cultures. There is a need for improved microbiology diagnostics and biomarkers of bacterial infection to permit accurate discrimination and improve antimicrobial stewardship.

A multicenter prospective observational study on the use of type and screen method versus conventional type and crossmatch policy for pre-transfusion testing in the Indian population

Despite knowing the benefits of the type and screen (TS) method in pre-transfusion testing (PTT), most transfusion centers in developing countries continue to be reluctant to adopt a TS strategy over the conventional type and antihuman globulin (AHG) crossmatch (TX) policy in their routine laboratory practice because of the cost of obtaining antibody screening reagents. To generate strong evidence, this multicenter, observational study was conducted in which we collected data prospectively over a 1-year period from six major blood centers in India. The primary objective of this study was to identify the discordance between TS and TX results. A secondary objective was to identify the allo-antibody specificity in patients with positive antibody detection tests. All patients with orders for red blood cell transfusion who met patient selection criteria were subjected to parallel testing by column agglutination technology (CAT) for both the antibody detection test (screen) using a commercial three-cell panel and for the AHG crossmatch. A total of 21,842 patients were tested. In 148 patients with incompatible crossmatches, samples from six patients gave negative results with the antibody detection test, whereas the antibody detection test was positive in samples from 118 patients among the 21,694 crossmatch-compatible cases. The TS approach achieved a positive percent agreement of 95.95 and was found to be significantly effective in preventing the transfusion of serologically incompatible blood. The risk associated with abbreviating the AHG crossmatch was found to be 0.009 percent. Most of the identified clinically significant alloantibodies were directed to Rh antigens (D>E>c>C>e), followed by anti-K and anti-M. This study has generated sufficient robust data for the Indian population by including patients from all major geographical areas of the country and concluded a satisfactory agreement level as well as non-inferiority to the current PTT policy. Therefore, TS policy can be implemented in developing countries with no compromise on blood safety, provided sufficient technical and infrastructural support are available.

A single dose of dietary nitrate supplementation protects against endothelial ischemia-reperfusion injury in early postmenopausal women

The onset of menopause and accompanying changes to ovarian hormones often precedes endothelial dysfunction in women. In particular, accelerated impairments in macrovascular and microvascular function coincide with the loss of estrogen, as does impaired endothelial responses to ischemia-reperfusion (IR) injury. In healthy, early postmenopausal women (n = 12; 3.9 ± 1.5 years since menopause) we tested the hypothesis that acute dietary nitrate (NO3-) supplementation would improve endothelial function and attenuate the magnitude of endothelial dysfunction following whole-arm IR in comparison with placebo. In this randomized, double-blind, placebo-controlled, crossover study we tested participants before and after NO3--rich (BRnitrate) and NO3--depleted (BRplacebo) beetroot juice (BR) consumption, as well as following IR injury, and 15 min after IR to assess recovery. Analyses with repeated-measures general linear models revealed a condition × time interaction for brachial artery flow-mediated dilation (FMD; P = 0.04), and no interaction effect was found for the near-infrared spectroscopy-derived reperfusion slope (P = 0.86). Follow-up analysis showed a significant decline in FMD following IR injury with BRplacebo in comparison with all other timepoints (all, P < 0.05), while this decline was not present with BRnitrate (all, P > 0.05). Our findings demonstrate that a single dose of dietary NO3- minimizes IR-induced macrovascular endothelial dysfunction in healthy, early postmenopausal women, but does not improve resting macrovascular and microvascular function. Trial registration number: NCT03644472. Novelty: In healthy, early postmenopausal women, a single dose of NO3--rich BR can protect against IR-induced endothelial dysfunction. This protection may be due to nitric oxide bioactivity during IR rather than improved endothelial function prior to the IR protocol per se.

Hypertriton Production in p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The study of nuclei and antinuclei production has proven to be a powerful tool to investigate the formation mechanism of loosely bound states in high-energy hadronic collisions. The first measurement of the production of _{Λ}^{3}H in p-Pb collisions at sqrt[s_{NN}]=5.02  TeV is presented in this Letter. Its production yield measured in the rapidity interval -1<y<0 for the 40% highest-multiplicity p-Pb collisions is dN/dy=[6.3±1.8(stat)±1.2(syst)]×10^{-7}. The measurement is compared with the expectations of statistical hadronization and coalescence models, which describe the nucleosynthesis in hadronic collisions. These two models predict very different yields of the hypertriton in charged particle multiplicity environments relevant to small collision systems such as p-Pb, and therefore the measurement of dN/dy is crucial to distinguish between them. The precision of this measurement leads to the exclusion with a significance larger than 6.9σ of some configurations of the statistical hadronization model, thus constraining the theory behind the production of loosely bound states at hadron colliders.

Polarization of Λ and Λ[over ¯] Hyperons along the Beam Direction in Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The polarization of the Λ and Λ[over ¯] hyperons along the beam (z) direction, P_{z}, has been measured in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV recorded with ALICE at the Large Hadron Collider (LHC). The main contribution to P_{z} comes from elliptic flow-induced vorticity and can be characterized by the second Fourier sine coefficient P_{z,s2}=⟨P_{z}sin(2φ-2Ψ_{2})⟩, where φ is the hyperon azimuthal emission angle and Ψ_{2} is the elliptic flow plane angle. We report the measurement of P_{z,s2} for different collision centralities and in the 30%-50% centrality interval as a function of the hyperon transverse momentum and rapidity. The P_{z,s2} is positive similarly as measured by the STAR Collaboration in Au-Au collisions at sqrt[s_{NN}]=200  GeV, with somewhat smaller amplitude in the semicentral collisions. This is the first experimental evidence of a nonzero hyperon P_{z} in Pb-Pb collisions at the LHC. The comparison of the measured P_{z,s2} with the hydrodynamic model calculations shows sensitivity to the competing contributions from thermal and the recently found shear-induced vorticity, as well as to whether the polarization is acquired at the quark-gluon plasma or the hadronic phase.

Impaired nuclear transport induced by juvenile ALS causing P525L mutation in NLS domain of FUS: A molecular mechanistic study

Amyotrophic lateral sclerosis (ALS) and fronto-temporal lobar degeneration (FTLD) are progressive neurological disorders affecting motor neurons. Cellular aggregates of fused in sarcoma (FUS) protein are found in cytoplasm of ALS and FTLD patients. Nuclear localisation signal (NLS) domain of FUS binds to Karyopherin β2 (Kapβ2), which drives nuclear transport of FUS from cytoplasm. Several pathogenic mutations are reported in FUS NLS, which are associated with its impaired nuclear transport and cytoplasmic mis-localisation. P525L mutation in NLS is most commonly found in cases of juvenile ALS (jALS), which affects individuals below 25 years of age. jALS progresses aggressively causing death within a year of its onset. This study elucidates the molecular mechanism behind jALS-causing P525L mutation hindering nuclear transport of FUS. We perform multiple molecular dynamics simulations in aqueous and hydrophobic solvent to understand the effect of the mutation at molecular level. Dynamics of Kapβ2-FUS complex is better captured in hydrophobic solvent compared to aqueous solvent. P525 and Y526 (PY-motif) of NLS exhibit fine-tuned stereochemical arrangement, which is essential for optimum Kapβ2 binding. P525L causes loss of several native contacts at interface leading to weaker binding, which promotes self-aggregation of FUS in cytoplasm. Native complex samples closed conformation, while mutant complex exhibits open conformation exposing hydrophilic residues of Kapβ2 to hydrophobic solvent. Mutant complex also fails to exhibit spring-like motion essential for its transport through nuclear pore complex. This study provides a mechanistic insight of binding affinity between NLS and Kapβ2 that inhibits self-aggregation of FUS preventing the disease condition.

Cambridge hybrid closed-loop algorithm in children and adolescents with type 1 diabetes: a multicentre 6-month randomised controlled trial

BACKGROUND

Closed-loop insulin delivery systems have the potential to address suboptimal glucose control in children and adolescents with type 1 diabetes. We compared safety and efficacy of the Cambridge hybrid closed-loop algorithm with usual care over 6 months in this population.

METHODS

In a multicentre, multinational, parallel randomised controlled trial, participants aged 6-18 years using insulin pump therapy were recruited at seven UK and five US paediatric diabetes centres. Key inclusion criteria were diagnosis of type 1 diabetes for at least 12 months, insulin pump therapy for at least 3 months, and screening HbA1c levels between 53 and 86 mmol/mol (7·0-10·0%). Using block randomisation and central randomisation software, we randomly assigned participants to either closed-loop insulin delivery (closed-loop group) or to usual care with insulin pump therapy (control group) for 6 months. Randomisation was stratified at each centre by local baseline HbA1c. The Cambridge closed-loop algorithm running on a smartphone was used with either (1) a modified Medtronic 640G pump, Medtronic Guardian 3 sensor, and Medtronic prototype phone enclosure (FlorenceM configuration), or (2) a Sooil Dana RS pump and Dexcom G6 sensor (CamAPS FX configuration). The primary endpoint was change in HbA1c at 6 months combining data from both configurations. The primary analysis was done in all randomised patients (intention to treat). Trial registration ClinicalTrials.gov, NCT02925299.

FINDINGS

Of 147 people initially screened, 133 participants (mean age 13·0 years [SD 2·8]; 57% female, 43% male) were randomly assigned to either the closed-loop group (n=65) or the control group (n=68). Mean baseline HbA1c was 8·2% (SD 0·7) in the closed-loop group and 8·3% (0·7) in the control group. At 6 months, HbA1c was lower in the closed-loop group than in the control group (between-group difference -3·5 mmol/mol (95% CI -6·5 to -0·5 [-0·32 percentage points, -0·59 to -0·04]; p=0·023). Closed-loop usage was low with FlorenceM due to failing phone enclosures (median 40% [IQR 26-53]), but consistently high with CamAPS FX (93% [88-96]), impacting efficacy. A total of 155 adverse events occurred after randomisation (67 in the closed-loop group, 88 in the control group), including seven severe hypoglycaemia events (four in the closed-loop group, three in the control group), two diabetic ketoacidosis events (both in the closed-loop group), and two non-treatment-related serious adverse events. There were 23 reportable hyperglycaemia events (11 in the closed-loop group, 12 in the control group), which did not meet criteria for diabetic ketoacidosis.

INTERPRETATION

The Cambridge hybrid closed-loop algorithm had an acceptable safety profile, and improved glycaemic control in children and adolescents with type 1 diabetes. To ensure optimal efficacy of the closed-loop system, usage needs to be consistently high, as demonstrated with CamAPS FX.

FUNDING

National Institute of Diabetes and Digestive and Kidney Diseases.

Measurement of the Groomed Jet Radius and Momentum Splitting Fraction in pp and Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

This article presents groomed jet substructure measurements in pp and Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector. The soft drop grooming algorithm provides access to the hard parton splittings inside a jet by removing soft wide-angle radiation. We report the groomed jet momentum splitting fraction, z_{g}, and the (scaled) groomed jet radius, θ_{g}. Charged-particle jets are reconstructed at midrapidity using the anti-k_{T} algorithm with resolution parameters R=0.2 and R=0.4. In heavy-ion collisions, the large underlying event poses a challenge for the reconstruction of groomed jet observables, since fluctuations in the background can cause groomed parton splittings to be misidentified. By using strong grooming conditions to reduce this background, we report these observables fully corrected for detector effects and background fluctuations for the first time. A narrowing of the θ_{g} distribution in Pb-Pb collisions compared to pp collisions is seen, which provides direct evidence of the modification of the angular structure of jets in the quark-gluon plasma. No significant modification of the z_{g} distribution in Pb-Pb collisions compared to pp collisions is observed. These results are compared with a variety of theoretical models of jet quenching, and provide constraints on jet energy-loss mechanisms and coherence effects in the quark-gluon plasma.

33 ECGs in the Surgical Patient - a Review of Practice

Aim

To Identify if baseline admission ECGs are performed for all emergency surgical patients over the age of 50 being admitted directly to General Surgery from the community. Aim to have 100% of patients &gt;50 years to have admission ECGs.

Method

We undertook a retrospective audit analysing the following parameters:

** This Hospital offers an in-hours (0900-1630, weekdays) ECG service via the cardiac physiology department.

We Conducted 3 cycles of 1 month duration each to assess findings.

Interventions:

Results

Cycle 1–50% (8/16) patients had admission ECGs. 50% (8/16) within 2 hours.

Cycle 2–54% (12/21) patients had admission ECGs. 43% (9/21) within 2 hours.

Cycle 3–71% (17/24) patients had admission ECGs. 62% (15/24) within 2 hours.

Conclusions

We noted improvement in admission ECGs through our interventions. Reminder emails were deemed useful. Barriers identified in After-hours ECGs being done on time due to clinical priorities. We identified a potential role for ECG-trained health-care professionals. 0900–1630 ECG service deemed valuable to admitting doctors. ECG machines were reviewed and found satisfactory. Possible delays in treatment could not be analysed with data collected. Hence, there is further scope to look into outcomes of delayed/missed ECGs e.g., delayed surgery / missed or alternative diagnosis.

Senior triaging of ENT emergency clinic referrals alleviates pressures on the outpatient department

INTRODUCTION

The ear, nose and throat (ENT) emergency clinic is managed by foundation year (FY) doctors from taking referrals to discharging patients, under the supervision of a registrar. FYs learn essential skills and knowledge on how to manage common ENT problems. The clinic is often overloaded because of a high patient demand, and this limits the opportunities for teaching. We hypothesised that the clinic bookings would be better managed if referrals from general practitioners (GPs) were triaged by registrars.

METHODS

Telephone referrals from GPs for the ENT emergency clinic were directed to the on-call ENT registrar, between 8am and 1pm from Monday to Friday, and to the FY outside of this period. Consecutive referrals to the emergency clinic were analysed in a baseline audit and a post-intervention cycle.

RESULTS

A total of 646 and 611 patients were given clinic appointments in the first and second cycles, respectively. Clinic session overbookings decreased from 85% to 46.3%. Appointments for referrals that were deemed inappropriate had reduced from 22% to 12.1%.

DISCUSSION AND CONCLUSION

Involvement of a registrar in taking referrals for the ENT emergency clinic was associated with a reduction in clinic overbookings. It is feasible and productive to involve a senior decision maker in the operational management of the emergency clinic, while preserving the delivery of this service by FYs for its training value.

From SARS-CoV-2 infection to COVID-19 morbidity: an in silico projection of virion flow rates to the lower airway via nasopharyngeal fluid boluses

Background: While the nasopharynx is initially the dominant upper airway infection site for SARS-CoV-2, the physiologic mechanism launching the infection at the lower airway is still not well-understood. Based on the rapidity of infection progression to the lungs, it has been hypothesized that the nasopharynx may be acting as the primary seeding zone for subsequent contamination of the lower airway via aspiration of virus-laden boluses of nasopharyngeal fluids. Methodology: To examine the plausibility of the aspiration-driven mechanism, we have computationally tracked the inhalation process in three anatomic airway reconstructions and have quantified the nasopharyngeal liquid volume transmitted to the lower airspace during each aspiration. Results: Extending the numerical trends on aspiration volume to earlier records on aspiration frequencies indicates a total aspirated nasopharyngeal liquid volume of 0.3 – 0.76 ml/day. Subsequently, for mean sputum viral load, our modeling projects that the number of virions reaching the lower airway will range over 2.1×106 – 5.3×106 /day; for peak viral load, the corresponding number hovers between 7.1×108 – 1.8×109. Conclusions: The virion transmission findings fill in a key piece of the mechanistic puzzle on the systemic progression of SARS-CoV-2, and subjectively point to health conditions like dysphagia, with proclivity to increased aspiration, as some of the potential underlying risk factors for aggressive lung infections.

Measurement of Prompt D^{0}, Λ_{c}^{+}, and Σ_{c}^{0,++}(2455) Production in Proton-Proton Collisions at sqrt[s]=13 TeV

The p_{T}-differential production cross sections of prompt D^{0}, Λ_{c}^{+}, and Σ_{c}^{0,++}(2455) charmed hadrons are measured at midrapidity (|y|<0.5) in pp collisions at sqrt[s]=13  TeV. This is the first measurement of Σ_{c}^{0,++} production in hadronic collisions. Assuming the same production yield for the three Σ_{c}^{0,+,++} isospin states, the baryon-to-meson cross section ratios Σ_{c}^{0,+,++}/D^{0} and Λ_{c}^{+}/D^{0} are calculated in the transverse momentum (p_{T}) intervals 2<p_{T}<12 and 1<p_{T}<24  GeV/c. Values significantly larger than in e^{+}e^{-} collisions are observed, indicating for the first time that baryon enhancement in hadronic collisions also extends to the Σ_{c}. The feed-down contribution to Λ_{c}^{+} production from Σ_{c}^{0,+,++} is also reported and is found to be larger than in e^{+}e^{-} collisions. The data are compared with predictions from event generators and other phenomenological models, providing a sensitive test of the different charm-hadronization mechanisms implemented in the models.

Measurement of the Cross Sections of Ξ_{c}^{0} and Ξ_{c}^{+} Baryons and of the Branching-Fraction Ratio BR(Ξ_{c}^{0}→Ξ^{-}e^{+}ν_{e})/BR(Ξ_{c}^{0}→Ξ^{-}π^{+}) in pp Collisions at sqrt[s]=13 TeV

The p_{T}-differential cross sections of prompt charm-strange baryons Ξ_{c}^{0} and Ξ_{c}^{+} were measured at midrapidity (|y|<0.5) in proton-proton (pp) collisions at a center-of-mass energy sqrt[s]=13  TeV with the ALICE detector at the LHC. The Ξ_{c}^{0} baryon was reconstructed via both the semileptonic decay (Ξ^{-}e^{+}ν_{e}) and the hadronic decay (Ξ^{-}π^{+}) channels. The Ξ_{c}^{+} baryon was reconstructed via the hadronic decay (Ξ^{-}π^{+}π^{+}) channel. The branching-fraction ratio BR(Ξ_{c}^{0}→Ξ^{-}e^{+}ν_{e})/BR(Ξ_{c}^{0}→Ξ^{-}π^{+})=1.38±0.14(stat)±0.22(syst) was measured with a total uncertainty reduced by a factor of about 3 with respect to the current world average reported by the Particle Data Group. The transverse momentum (p_{T}) dependence of the Ξ_{c}^{0}- and Ξ_{c}^{+}-baryon production relative to the D^{0} meson and to the Σ_{c}^{0,+,++}- and Λ_{c}^{+}-baryon production are reported. The baryon-to-meson ratio increases toward low p_{T} up to a value of approximately 0.3. The measurements are compared with various models that take different hadronization mechanisms into consideration. The results provide stringent constraints to these theoretical calculations and additional evidence that different processes are involved in charm hadronization in electron-positron (e^{+}e^{-}) and hadronic collisions.

Λ_{c}^{+} Production and Baryon-to-Meson Ratios in pp and p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV at the LHC

The prompt production of the charm baryon Λ_{c}^{+} and the Λ_{c}^{+}/D^{0} production ratios were measured at midrapidity with the ALICE detector in pp and p-Pb collisions at sqrt[s_{NN}]=5.02  TeV. These new measurements show a clear decrease of the Λ_{c}^{+}/D^{0} ratio with increasing transverse momentum (p_{T}) in both collision systems in the range 2<p_{T}<12  GeV/c, exhibiting similarities with the light-flavor baryon-to-meson ratios p/π and Λ/K_{S}^{0}. At low p_{T}, predictions that include additional color-reconnection mechanisms beyond the leading-color approximation, assume the existence of additional higher-mass charm-baryon states, or include hadronization via coalescence can describe the data, while predictions driven by charm-quark fragmentation processes measured in e^{+}e^{-} and e^{-}p collisions significantly underestimate the data. The results presented in this Letter provide significant evidence that the established assumption of universality (colliding-system independence) of parton-to-hadron fragmentation is not sufficient to describe charm-baryon production in hadronic collisions at LHC energies.

Experimental Evidence for an Attractive p-ϕ Interaction

This Letter presents the first experimental evidence of the attractive strong interaction between a proton and a ϕ meson. The result is obtained from two-particle correlations of combined p-ϕ⊕ p[over ¯]-ϕ pairs measured in high-multiplicity pp collisions at sqrt[s]=13  TeV by the ALICE Collaboration. The spin-averaged scattering length and effective range of the p-ϕ interaction are extracted from the fully corrected correlation function employing the Lednický-Lyuboshits approach. In particular, the imaginary part of the scattering length vanishes within uncertainties, indicating that inelastic processes do not play a prominent role for the p-ϕ interaction. These data demonstrate that the interaction is dominated by elastic p-ϕ scattering. Furthermore, an analysis employing phenomenological Gaussian- and Yukawa-type potentials is conducted. Under the assumption of the latter, the N-ϕ coupling constant is found to be g_{N-ϕ}=0.14±0.03(stat)±0.02(syst). This work provides valuable experimental input to accomplish a self-consistent description of the N-ϕ interaction, which is particularly relevant for the more fundamental studies on partial restoration of chiral symmetry in nuclear medium.