On-Resin Photochemical Decarboxylative Arylation of Peptides

Here we describe the application of photochemical decarboxylative arylation as a late-stage functionalization reaction for peptides. The reaction uses redox-active esters of aspartic acid and glutamic acid on the solid phase to provide analogues of aromatic amino acids. By using aryl bromides as arylation reagents, a wide variety of amino acids can be accessed without having to synthesize them individually in solution. The reaction is compatible with proteinogenic amino acids and was used to perform a structure-activity relationship study of a PRMT5 binding peptide.

Muscle coactivation during gait in children with and without cerebral palsy

BACKGROUND

Children with Cerebral Palsy (CP) walk with an uncoordinated gait compared to Typically Developing (TD) children. This behavior may reflect greater muscle co-activation in the lower limb; however, findings are inconsistent, and the determinants of this construct are unclear.

RESEARCH OBJECTIVES

(i) Compare lower-limb muscle co-activation during gait in children with, and without CP, and (ii) determine the extent to which muscle co-activation is influenced by electromyography normalization procedures and Gross Motor Function Classification System (GMFCS) class.

METHODS

An electromyography system measured muscle activity in the rectus femoris, semitendinosus, gastrocnemius, and tibialis anterior muscles during walking in 46 children (19 CP, 27 TD). Muscle co-activation was calculated for the tibialis anterior-gastrocnemius (TA-G), rectus femoris-gastrocnemius (RF-G), and rectus femoris-semitendinosus (RF-S) pairings, both using root mean squared (RMS)-averaged and dynamically normalized data, during stance and swing. Mann-Whitney U and independent t-tests examined differences in muscle co-activation by group (CP vs. TD) and GMFCS class (CP only), while mean difference 95% bootstrapped confidence intervals compared electromyography normalization procedures.

RESULTS

Using dynamically normalized data, the CP group had greater muscle co-activation for the TA-G and RF-G pairs during stance (p < 0.01). Using RMS-averaged data, the CP group had greater muscle co-activation for TA-G (stance and swing, p < 0.01), RF-G (stance, p < 0.05), and RF-S (swing, p < 0.01) pairings. Muscle co-activation calculated with dynamically normalized, compared to RMS-averaged data, were larger in the RF-S and RF-G (stance) pairs, but smaller during swing (RF-G). Children with CP classified as GMFCS II had greater muscle co-activation during stance in the TA-G pair (p < 0.05).

SIGNIFICANCE

Greater muscle co-activation observed in children with CP during stance may reflect a less robust gait strategy. Although data normalization procedures influence muscle co-activation ratios, this behavior was observed independent of normalization technique.

Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding

The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.

First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9  GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36  GeV/c^{2}, rejecting cross sections above 9.2×10^{-48}  cm at the 90% confidence level.

A Fokker-Planck Framework for Parameter Estimation and Sensitivity Analysis in Colon Cancer

A new stochastic framework for parameter estimation and uncertainty quantification in colon cancer-induced immune response is presented. The dynamics of colon cancer is given by a stochastic process that captures the inherent randomness in the system. The stochastic framework is based on the Fokker-Planck equation that represents the evolution of the probability density function corresponding to the stochastic process. An optimization problem is formulated that takes input individual patient data with randomness present, and is solved to obtain the unknown parameters corresponding to the individual tumor characteristics. Furthermore, sensitivity analysis of the optimal parameter set is performed to determine the parameters that need to be controlled, thus, providing information of the type of drugs that can be used for treatment.

P-105 Genetic variants in the spermatogenic transcription regulators RFX2 and TAF7 enhance the incidence of azoospermia

Study question

What are the genetic variants of meiotic regulator genes that are implicated in male infertility among men from West Bengal, India?

Summary answer

TAF7 C16T (MW827584 G &gt; A) and RFX2 562delT (MZ560629delA) new variations may have a major impact on optimal fertility in men from West Bengal.

What is known already

According to published research, roughly 50% of reported infertility cases in India are due to male reproductive abnormalities. Because of the involvement of several gene regulatory networks in the spermatogenesis process, the genetic etiology of idiopathic male infertility remains a mystery. The AZF region of the Y chromosome microdeletion has been discovered as a prevalent cause of male infertility across all ethnicities. Infertility in men has also been linked to sex chromosomal copy number variation and autosomal gene polymorphisms.

Study design, size, duration

This is a case-control study to infer whether the genetic variants are significantly associated in favor of cases or in favor of controls. The study included 160 healthy male controls and 150 azoospermic cases submitted to the Institute of Reproductive Medicine in Kolkata (IRM). All of the subjects agreed to participate in the study and provided blood and sperm samples. The duration of the study is three years. Seminograms were made to filter azoospermic individuals.

Participants/materials, setting, methods

2 ml of venous blood samples were taken from azoospermic men using the venipuncture procedure and stored in EDTA coated vacutainer tubes at -20°C for DNA isolation.QIAamp Blood Mini Kit was used to isolate genomic DNA. For PCR analysis, unique primers for TAF7 and RFX2 functional domains were created. Taq Dye Deoxy Terminator sequencing kit (Applied Biosystems, Foster City, USA) and ABI Prism 377 DNA sequencer were used to analyze PCR results.

Main results and the role of chance

We have found two significant genetic alterations in the coding region of TAF7 and RFX2 which are MW827584 G &gt; A(C16T) and MZ560629delA(562delT) respectively. Both were found to have a strong association to the occurrence of azoospermia. For MW827584 G &gt; A, minor allele ‘A’ has shown elevated risk of azoospermic against the odd 4.684 (95% C.I = 2.900-7.564, Relative risk =2.110, p value = &lt;0.001). Fisher’s exact test was performed to calculate Odds ratios with respective 95% confidence interval (CI). After Bonferroni's correction, a two-tailed P-value of less than 0.02 was considered statistically significant throughout. Only the case sample cohort had the RFX2 deletion MZ560629 delA. Only 9 cases with this unique deletion in heterozygous form were found out of 150 azoospermic patients. This frameshift mutation results in the production of an early termination signal at exon 6, resulting in the creation of a truncated protein. The wild-type RFX2 protein has 729 amino acids but this frameshift mutation results in a 212-amino-acid RFX2 protein that lacks several secondary motifs and domains, rendering the wild-type function useless. In silico analysis of SIFT, PROVEAN, MUTATION TASTER and REGULATION SPOTTER predicted that these genetic variants are disease-causing.

Limitations, reasons for caution

There are some potential limitations to our research. A larger sample size investigation is needed to reconfirm the genetic association study. Moreover, confounding effects of allelic variation of those genetic modifiers may cause differences in the manifestation of fertility state along with the allelic variants of TAF7 and RFX2 genes.

Wider implications of the findings

This diagnostic technique will not only reduce the hazards connected with assisted reproductive technologies (ART), but it will also provide insight into previously unknown areas of infertility and enable clinicians in conducting a more thorough investigation of the patients.

Trial registration number

not applicable

RNA-Binding Macrocyclic Peptides

Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.

First Direct Detection Constraints on Planck-Scale Mass Dark Matter with Multiple-Scatter Signatures Using the DEAP-3600 Detector

Dark matter with Planck-scale mass (≃10^{19}  GeV/c^{2}) arises in well-motivated theories and could be produced by several cosmological mechanisms. A search for multiscatter signals from supermassive dark matter was performed with a blind analysis of data collected over a 813 d live time with DEAP-3600, a 3.3 t single-phase liquid argon-based detector at SNOLAB. No candidate signals were observed, leading to the first direct detection constraints on Planck-scale mass dark matter. Leading limits constrain dark matter masses between 8.3×10^{6} and 1.2×10^{19}  GeV/c^{2}, and ^{40}Ar-scattering cross sections between 1.0×10^{-23} and 2.4×10^{-18}  cm^{2}. These results are interpreted as constraints on composite dark matter models with two different nucleon-to-nuclear cross section scalings.

The Impact of the COVID-19 Pandemic on Creutzfeldt-Jakob Disease Surveillance and Patient Care in the United Kingdom

Background and purpose

Creutzfeldt–Jakob disease (CJD) is lethal and transmissible. We assessed the impact of the COVID‐19 pandemic on UK CJD surveillance. We hypothesized that (i) disruptions prolonged diagnostic latency; (ii) autopsy rates declined; and (iii) COVID‐19 infection negatively affected diagnosis, care, and survival.

Methods

We retrospectively investigated the first year of the pandemic, using the preceding year as a comparator, quantifying numbers of individuals assessed by the UK National CJD Research & Surveillance Unit for suspected CJD, time to diagnosis, disease duration, and autopsy rates. We evaluated the impact of COVID‐19 status on diagnosis, care, and survival in CJD.

Results

A total of 148 individuals were diagnosed with CJD in the pandemic (from a total of 166 individuals assessed) compared to 141 in the comparator (from 145 assessed). No differences were identified in disease duration or time to diagnosis. Autopsy rates were unchanged. Twenty individuals had COVID‐19; 60% were symptomatic, and 10% had severe disease. Disruptions in diagnosis and care were frequently identified. Forty percent of COVID‐19‐positive individuals died; however, COVID‐19 status did not significantly alter survival duration in CJD.

Conclusions

The COVID‐19 pandemic has not impacted UK CJD case ascertainment or survival, but diagnostic evaluation and clinical care of individuals have been affected.

α-Helices propagating from stable nucleators exhibit unconventional thermal folding

Although the effect of thermal perturbations on protein structure has long been modeled in helical peptides, several details, such as the relation between the thermal stabilities of the propagating and nucleating segments of helices, remain elusive. We had earlier reported on the helix-nucleating propensities of covalent H-bond surrogate-constrained α-turns. Here, we analyze the thermal stabilities of helices that propagate along peptides appended to these α-helix nucleators using their NMR and far-UV CD spectra. Unconventional thermal folding of these helix models reveals that the helical fold in propagating backbones resists thermal perturbations as long as their nucleating template is intact. The threshold temperature of such resistance is also influenced by the extent of similarity between the natures of helical folds in the nucleating and propagating segments. Correlations between helicities and rigidities of helix-nucleating and helix-propagating segments reveal subtle interdependence, which explains cooperativity and residual helix formation during protein folding.

A randomized controlled trial of restricted versus standard fluid management in late preterm and term infants with transient tachypnea of the newborn

BACKGROUND

Transient tachypnea of the newborn(TTNB) is the most common respiratory morbidity in late preterm and term babies and is pathophysiologically related to delayed lung fluid clearance after birth. Mimicking low physiological fluid intake in the initial period of life may accelerate the recovery from TTNB. In a randomized controlled trial, we compared the roles of restricted versus standard fluid management in babies with TTNB requiring respiratory support.

METHODS

This parallel group,non-blinded, stratified randomized controlled trial was conducted in a level III neonatal unit of eastern India. Late preterm and term babies with TTNB requiring continuous positive airway pressure (CPAP) were randomly allocated to standard and restricted fluid arms for the first 72 hours (hrs). Primary outcome was CPAP duration.

RESULTS

In total, 100 babies were enrolled in this study with 50 babies in each arm. CPAP duration was significantly less in the restricted arm (48[42, 54] hrs vs 54[48,72] hrs, p = 0.002). However, no difference was observed in the incidence of CPAP failure between the two arms. In the subgroup analysis, the benefit of reduced CPAP duration persisted in late preterm but not in term infants. However, the effect was not significant in the late preterm babies exposed to antenatal steroid.

CONCLUSION

This trial demonstrated the safety and effectiveness of restrictive fluid strategy in reducing CPAP duration in late preterm and term babies with TTNB. Late preterm babies, especially those not exposed to antenatal steroid were the most benefitted by this strategy.

Pulse-shape discrimination against low-energy Ar-39 beta decays in liquid argon with 4.5 tonne-years of DEAP-3600 data

The DEAP-3600 detector searches for the scintillation signal from dark matter particles scattering on a 3.3 tonne liquid argon target. The largest background comes from 39 Ar beta decays and is suppressed using pulse-shape discrimination (PSD). We use two types of PSD estimator: the prompt-fraction, which considers the fraction of the scintillation signal in a narrow and a wide time window around the event peak, and the log-likelihood-ratio, which compares the observed photon arrival times to a signal and a background model. We furthermore use two algorithms to determine the number of photons detected at a given time: (1) simply dividing the charge of each PMT pulse by the mean single-photoelectron charge, and (2) a likelihood analysis that considers the probability to detect a certain number of photons at a given time, based on a model for the scintillation pulse shape and for afterpulsing in the light detectors. The prompt-fraction performs approximately as well as the log-likelihood-ratio PSD algorithm if the photon detection times are not biased by detector effects. We explain this result using a model for the information carried by scintillation photons as a function of the time when they are detected.

"In-vitro Effects of Chlorpyrifos and Monocrotophos on the Activity of Acetylcholinesterase (AChE) in Different Tissues of Apple Snail Pila globosa (Swainson, 1822)"

The impact of two organophosphorus insecticides [Chlorpyrifos (CPF) and Monocrotophos (MCP)] on non-target wild natural gastropod, Pila globosa (apple snail) from the paddy fields was studied. The activity of acetylcholinesterase (AChE) was monitored on foot-muscle and hepatopancreas tissues of control and exposed snails. In the foot- muscle AChE inhibition progressed and reached 54.19% and 63.13% of the control, whereas, the AChE inhibition in the hepatopancreas reached 46.96% and 53.67% over control after 48 hours of exposure to 1.5 mL.L-1 and 2.5 mL.L-1 CPF respectively. After 48 hours of MCP exposure at 1.5 mL.L-1 and 2.5 mL.L-1 separately, the AChE inhibition of foot muscle was 49.07% and 57.59% respectively while in hepatopancreas it was 44.65% and 48.84% respectively. Our results show more inhibition of AChE activities on the foot-muscle than hepatopancreas in a concentration and time-dependent manner with greater severity by CPF in comparison to MCP. AChE inhibition increased with the increasing exposure time.

A prospective cohort study on predictors of mortality of delirium in an emergency observational unit

BACKGROUND

Delirium is often an underdiagnosed and underestimated neuropsychiatric syndrome, especially in low- and middle-income countries.

AIM

To document the prevalence and clinical profile of delirium and to detect the baseline parameters associated with in-hospital mortality.

DESIGN

A prospective cohort study conducted between January 2016 to December 2016 at an adult medical emergency observational unit of an academic hospital in north India.

METHODS

Confusion Assessment Method for the intensive care unit was used for screening and diagnosis of delirium. Subtypes of delirium and severity were defined with the Richmond agitation-sedation scale and Delirium Rating Scale-Revised-98 (DRS-R-98).

RESULTS

Out of 939 screened patients, 312 (33.2%) had delirium, including 73.7% unrecognized cases. The mean age was 49.1 ± 17.3 years (range 17-90), and only 33.3% of the patients were above 60 years. The prevalence of hypoactive, mixed and hyperactive delirium was 39.1, 33.7 and 27.2%, respectively. Usual predisposing factors were alcohol use disorder (57.4%) and hypertension (51.0%), and infections remain the most common precipitating factors (42.0%). In total, 96.1% of patients received midazolam before delirium onset, and physical restraints were used in 73.4%. Mortality was higher in delirium (19.9% vs. 6.4%). The independent predictors of death in delirium were low diastolic blood pressure (P-value = 0.000), Glasgow coma scale score <15 (P = 0.026), high Acute Physiology and Chronic Health Evaluation II score (P = 0.007), high DRS-R-98 severity score (P = 0.000) and hyperactive delirium (P = 0.024).

CONCLUSION

Rapid screening with Confusion Assessment Method for the intensive care unit detected a high prevalence of delirium (even in young patients), and it associated with high mortality.

Atmospheric Carbon and Transport - America (ACT-America) Data Sets: Description, Management, and Delivery

The ACT-America project is a NASA Earth Venture Suborbital-2 mission designed to study the transport and fluxes of greenhouse gases. The open and freely available ACT-America data sets provide airborne in situ measurements of atmospheric carbon dioxide, methane, trace gases, aerosols, clouds, and meteorological properties, airborne remote sensing measurements of aerosol backscatter, atmospheric boundary layer height and columnar content of atmospheric carbon dioxide, tower-based measurements, and modeled atmospheric mole fractions and regional carbon fluxes of greenhouse gases over the Central and Eastern United States. We conducted 121 research flights during five campaigns in four seasons during 2016-2019 over three regions of the US (Mid-Atlantic, Midwest and South) using two NASA research aircraft (B-200 and C-130). We performed three flight patterns (fair weather, frontal crossings, and OCO-2 underflights) and collected more than 1,140 h of airborne measurements via level-leg flights in the atmospheric boundary layer, lower, and upper free troposphere and vertical profiles spanning these altitudes. We also merged various airborne in situ measurements onto a common standard sampling interval, which brings coherence to the data, creates geolocated data products, and makes it much easier for the users to perform holistic analysis of the ACT-America data products. Here, we report on detailed information of data sets collected, the workflow for data sets including storage and processing of the quality controlled and quality assured harmonized observations, and their archival and formatting for users. Finally, we provide some important information on the dissemination of data products including metadata and highlights of applications of ACT-America data sets.

Efficacy and correlative analyses of avelumab plus axitinib versus sunitinib in sarcomatoid renal cell carcinoma: post hoc analysis of a randomized clinical trial

BACKGROUND

Among patients with advanced renal cell carcinoma (RCC), those with sarcomatoid histology (sRCC) have the poorest prognosis. This analysis assessed the efficacy of avelumab plus axitinib versus sunitinib in patients with treatment-naive advanced sRCC.

METHODS

The randomized, open-label, multicenter, phase III JAVELIN Renal 101 trial (NCT02684006) enrolled patients with treatment-naive advanced RCC. Patients were randomized 1 : 1 to receive either avelumab plus axitinib or sunitinib following standard doses and schedules. Assessments in this post hoc analysis of patients with sRCC included efficacy (including progression-free survival) and biomarker analyses.

RESULTS

A total of 108 patients had sarcomatoid histology and were included in this post hoc analysis; 47 patients in the avelumab plus axitinib arm and 61 in the sunitinib arm. Patients in the avelumab plus axitinib arm had improved progression-free survival [stratified hazard ratio, 0.57 (95% confidence interval, 0.325-1.003)] and a higher objective response rate (46.8% versus 21.3%; complete response in 4.3% versus 0%) versus those in the sunitinib arm. Correlative gene expression analyses of patients with sRCC showed enrichment of gene pathway scores for cancer-associated fibroblasts and regulatory T cells, CD274 and CD8A expression, and tumors with The Cancer Genome Atlas m3 classification.

CONCLUSIONS

In this subgroup analysis of JAVELIN Renal 101, patients with sRCC in the avelumab plus axitinib arm had improved efficacy outcomes versus those in the sunitinib arm. Correlative analyses provide insight into this subtype of RCC and suggest that avelumab plus axitinib may increase the chance of overcoming the aggressive features of sRCC.

Hydrogen Bond Surrogate-Constrained Dynamic Antiparallel β-Sheets

Antiparallel β-sheets are important secondary structures within proteins that equilibrate with random-coil states; however, little is known about the exact dynamics of this process. Here, the first dynamic β-sheet models that mimic this equilibrium have been designed by using an H-bond surrogate that introduces constraint and torque into a tertiary amide bond. 2D NMR data sufficiently reveal the structure, kinetics, and thermodynamics of the folding process, thereby leading the way to similar analysis in isolated biologically relevant β-sheets.

Mid-term follow-up of percutaneous access for standard and complex EVAR using the ProGlide device

OBJECTIVES

Endovascular Aneurysm Repair is an established treatment for abdominal aortic aneurysm which requires arterial access via the groin. Most centres perform percutaneous ultrasound-guided access into the common femoral artery for delivery of the stent graft. The profile of endovascular devices necessitates large sheath sizes, therefore formal closure of the arterial puncture site is required. Various percutaneous devices are available, with data lacking on efficacy and mid-term safety profile. We present outcomes from a single centre with the Perclose ProGlide™ (Abbott Vascular Devices, CA, USA) suture-mediated system, using the well described "pre-close" technique.

MATERIALS & METHODS

Data were collected from operative records and electronic medical records. Patients undergoing standard (EVAR) or complex (F/B-EVAR) aneurysm repair between March 2015 and September 2019 were included. Complications were recorded per-patient and per-groin procedure.

RESULTS

266 patients were included; 182 (68.4%) standard infrarenal EVAR, 84 (31.6%) F/B-EVAR. There were a total of 484 groin procedures performed. Intraoperative Perclose ProGlide™ success was 98.1% (per patient) or 99.0% (per groin procedure). 30-day groin complication rate was 6.1% (per patient) or 3.1% (per groin procedure). There were no pre- or peri-operative factors which predicted the occurrence of groin complications. The rate of groin complications was not related to sheath size.

CONCLUSIONS

Our data support the use of percutaneous access with a pre-close technique for a variety of endovascular aneurysm repair procedures with both large- and small-bore access. The Perclose ProGlide™ system provides excellent mid-term complication-free and reintervention-free outcomes for groin procedures.

Shock wave propagation through air: a reactive molecular dynamics study

Shock compression of air is observed in numerous situations ranging from explosions to hypersonic vehicle entry into atmosphere. In an effort to develop continuum-based equation of state for air subjected to shock compression, it is necessary to understand the dynamics of the shock compression process with regards to formation of new chemical species in air at the molecular level. With this in perspective, three different models of air (consisting a mixture of O 2 , N 2 and CO 2 gas, with or without H 2 O based on presence of humidity) are subjected to shock compression ranging from 0.5 km s −1 to 5.0 km s −1 particle velocities. Thermodynamic quantities are evaluated to plot Rankine Hugoniot planes for the three different air models: dry air at mean sea level (MSL), humid air at MSL and dry air at high altitude level of 36 000 ft above MSL. It is observed that high shock velocities eventually results in dissociation of gaseous molecules and formation of new gaseous species which has been quantified in the manuscript.

Morphology of enteric glia in colorectal carcinoma: A comparative study of tumor site and its proximal normal margin

OBJECTIVE

Colorectal carcinoma (CRC) is the third most common cancer in the world and fifth most common cancer in India. To understand the extent of perineural invasion (PNI) in CRC it is essential to study the morphology of enteric glial cells (EGCs). The aim of the study was to analyze the numerical density of EGCs and area of myenteric ganglia (MG) in the colonic tissue samples collected from CRC patients.

MATERIAL AND METHODS

Fifteen intraoperative tissue specimens were collected from the tumor site and 2cm proximal to the upper extent of tumor. The samples were divided into four groups: group 1 (n=15): proximal tumor free colonic tissue; group 2 (n=3): well-differentiated; group 3 (n=8): moderately differentiated; group 4 (n=4): poorly differentiated adenocarcinoma. After processing the tissues were subjected to hematoxylin and eosin staining. The anti-S100β and anti-GFAP antibodies were used to observe the EGCs.

RESULTS

In the H&E stained sections the number of myenteric ganglia appeared to be decreasing with increasing grade of adenocarcinoma. Immunostaining showed significant decreasing pattern in the numerical density of EGCs per myenteric ganglion and mean area of myenteric ganglia in relation to the thickness of circular muscle, corresponding to the increasing grades of adenocarcinoma. The morphology of the EGCs remained unaltered in the colonic tissue adjacent to the tumor site.

CONCLUSION

Significant loss of EGCs and neurodegeneration corresponded with the grade of tumor emphasizing on its prognostic value. The PNI was not seen in the clear margin proximal to the tumor site.

Microarray based gene expression profiling of advanced gall bladder cancer

BACKGROUND

Gall bladder cancer (GBC) is an aggressive cancer with specific predilection like female gender and specific geographical areas, however the molecular mechanisms and factors contributing to the clinical or biological behavior are not understood.

AIM

The aim of this study was to perform a comprehensive analysis of differentially expressed genes in advanced GBC and chronic cholecystitis (CC) cases.

MATERIALS AND METHODS

Microarray was planned on fresh specimens of advanced GBC and CC cases using single color cRNA based microarray technique (8X60K format; Agilent Technologies, USA). Twelve advanced GBC and four CC patients were included in the study.

RESULTS

Of the total of 1307 differentially expressed genes, 535 genes were significantly upregulated, while 772 genes were significantly downregulated in advanced GBC vs CC samples. Differentially expressed genes were associated with biological processes (55.03%), cellular components (31.48%), and molecular functions (13.49%) respectively. The important pathways or key processes affected were cell cycle, DNA replication, oxidative stress, gastric cancer pathway. Using in silico analysis tools, three differentially expressed genes i.e. TPX2, Cdc45 and MCM4 were selected (for their significant role in DNA replication and microtubule function) and were further validated in 20 advanced GBC cohort by immunohistochemistry. Significant positive association of Cdc45 and MCM4 proteins was found in advanced GBC cases (p = 0.043), suggesting the probable oncogenic role of Cdc45 and MCM4 proteins in advanced GBC.

CONCLUSION

Our data demonstrate the potential regulation of Cdc45-MCM4 axis in advanced GBC tumors. Additionally, our study also revealed a range of differentially expressed genes (e.g. TPX2, AKURA etc.) between GBC and CC, and further validation of these genes might provide a potential diagnostic or therapeutic target in future.

Helix-Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth

A detailed understanding of forces guiding the rapid folding of a polypeptide from an apparently random coil state to an ordered α-helical structure following the rate-limiting preorganization of the initial three residue backbones into helical conformation is imperative to comprehending and regulating protein folding and for the rational design of biological mimetics. However, several details of this process are still unknown. First, although the helix-coil transition was proposed to originate at the residue level (J. Chem. Phys. 1959, 31, 526-535; J. Chem. Phys. 1961, 34, 1963-1974), all helix-folding studies have only established it between time-averaged bulk states of a long-lived helix and several transiently populated random coils, along the whole helix model sequence. Second, the predominant thermodynamic forces driving either this two-state transition or the faster helix growth following helix nucleation are still unclear. Third, the conformational space of the random coil state is not well-defined unlike its corresponding α-helix. Here we investigate the restrictions placed on the conformational space of a Gly residue backbone, as a result of it immediately succeeding a nascent α-helical turn. Analyses of the temperature-dependent 1D-, 2D-NMR, FT-IR, and CD spectra and GROMACS MD simulation trajectory of a Gly residue backbone following a model α-helical turn, which is artificially rigidified by a covalent hydrogen bond surrogate, reveal that: (i) the α-helical turn guides the ϕ torsion of the Gly exclusively into either a predominantly populated entropically favored α-helical (α-ϕ) state or a scarcely populated random coil (RC-ϕ) state; (ii) the α-ϕ state of Gly in turn favors the stability of the preceding α-helical turn, while the RC-ϕ state disrupts it, revealing an entropy-driven synergetic guidance for helix growth in the residue following helix nucleation. The applicability of a current synergetic guidance mechanism to explain rapid helix growth in folded and unfolded states of proteins and helical peptides is discussed.

H-Bond Surrogate-Stabilized Shortest Single-Turn α-Helices: sp2 Constraints and Residue Preferences for the Highest α-Helicities

Short α-helical sequences of proteins fail to maintain their native conformation when taken out of their protein context. Several covalent constraints have been designed, including the covalent H-bond surrogate (HBS)-where a peptide backbone i + 4 → i H-bond is replaced by a covalent surrogate-to nucleate α-helix in short sequences (>7 < 15 amino acids). But constraining the shortest sequences (four amino acids) into a single α-helical turn is still a significant challenge. Here, we introduce an HBS model that can be placed in unstructured tetrapeptides without excising any of its residues, and that biases them predominantly into remarkably stable single α-helical turns in varying solvents, pH values, and temperatures. Circular dichroism (CD), Fourier transform infrared (FT-IR) absorption, one-dimensional (1D)-NMR, two-dimensional (2D)-NMR spectral and computational analyses of the HBS-constrained tetrapeptide analogues reveal that (a) the number of sp² atoms in the HBS-constrained backbone influences their predominance and rigidity in the α-helical conformation; and (b) residue preferences at the unnatural HBS-constrained positions influence their α-helicities, with Moc[GFA]G-OMe (1a) showing the highest known α-helicity (θ_n→π*MRE ∼-25.3 × 10³ deg cm² dmol^-1 at 228 nm) for a single α-helical turn. Current findings benefit chemical biological applications desiring predictable access to single α-helical turns in tetrapeptides.

Multimodality treatment of intracranial arteriovenous malformations in South Island, New Zealand

Treatment of intracranial arteriovenous malformations is complex and multidisciplinary. This article presents the treatment model utilized in Christchurch, New Zealand which provides cerebrovascular surgery and interventional neuroradiology to the entire south island (approximate population of 1.1 million). A total of 40 patients treated over a 10 year period (2004-2014) are analysed here. Nine patients were managed surgically and complete resection was achieved in 100% of cases. Permanent mortality was 0% and permanent morbidity was 22% however median mRS improved from 3.0 preoperatively to 1.0 at follow up. Embolisation was utilized in 31 patients (mean age 40), of which 45% presented with haemorrhage, 39% with seizures, 10% with a headache only, and 6% with a deficit. None were found incidentally. The Spetzler-Martin grade 1 cases accounted for 10% of the cohort, 23% were grade II, 42% grade III, 23% grade IV and 3% grade V. A single aneurysm was present in 42% of cases, and multiple in 13%. The nidus was obliterated in 9.6% of cases with a morbidity rate of 6.5% and mortality rate of 3%. Modified Rankin scale improved marginally from 0.9 at diagnosis to 0.88 at final follow up (mean 22 months). There were no cases of recanalization. The total nidus obliteration rate using our algorithm of surgery alone for small accessible lesions, then staged embolization for larger lesions with adjuvant radiosurgery reserved for cases with residual nidus, was 50%.

Studying land use dynamics using decadal satellite images and Dyna-CLUE model in the Mahanadi River basin, India

Population growth rate indicates the proportional rate of settlement expansion and landscape modification in any river basin. The Mahanadi River basin (MRB), which is a densely populated, cropland and forest-dominated landscape, is selected as a case study area for studying the nature of built-up expansion and the corresponding land cover modifications. Satellite data-derived land use/land cover (LU/LC) maps for the years 1995, 2005, and 2015 were used for identification of landscape changes during the past three decades. One of the major LU/LC changes are observed in terms of increase in the water, which may be attributed to construction of new dams at the cost of the croplands and forest areas. Conversion of forest to cropland and expansion and densification of built-up areas in and around the existing built-up areas are also identified as a major LU/LC change. The geostatistical analysis was performed to identify the relationship between LU/LC classes with drivers, which showed that built-up areas were more in topographically flat terrain with higher soil depth, and expanded more around the existing built-up areas; cropland areas were more at lower elevation and less sloppy terrain, and forest areas were more at higher elevation. The LU/LC scenario of 2025 was projected using a spatially explicit dynamic conversion of land use and its effects (Dyna-CLUE) modeling platform with the LU/LC change trends of past 10 years (2005-2015) and 20 years (1995-2015). The major LU/LC changes observed during 2005-2015 were built-up expansion by 36.53% and deciduous forest and cropland reduction by 0.35% and 0.45%, respectively. Thus, the corresponding predicted change during 2015-2025 estimated built-up expansion by 25.70% and deciduous forest and croplands loss by 0.43% and 0.35%, respectively. On the other hand, during 1995 to 2015, the total built-up expansion and deciduous forest and cropland reduction were observed 50.79%, 0.45%, and 0.73%, respectively. Thus, the predicted changes during 2015-2025 were estimated as 18.48% built-up expansion and 0.22% and 0.21% deciduous forest and cropland loss. However, with the conditions of restricted deforestation and less landscape modification, the LU/LC projections show less built-up area expansion, reducing the cropland, fallow land, plantation, and waste land. The reduced numbers of land cover conversions types during 2005-2015 compared with 1995-2005 indicate more stabilized landscape. The input LU/LC maps and statistical analysis demonstrated the landscape modifications and causes observed in the basin. The model projected LU/LC maps are giving insights to possible changes under multiple pathways, which will help the agriculture, forest, urban, and water resource planners and managers in improved policy-making processes.

Exploring the structure of Xe isotopes in A ~ 130 region: Single particle and collective excitations

High and medium spin structures of 130,131Xe have been studied using α-induced fusion-evaporation reaction and the Indian National Gamma Array (INGA) coupled with a digital data acquisition system. Various new band structures and near yrast levels of 131Xe have been established. The multipolarities of the observed transitions have been assigned on the basis of the DCO ratios and the polarization asymmetry measurements. Band structures based on 1-quasi-particle (qp), 3-qp configurations have been observed. A new Magnetic Rotational (MR) band based on 5-qp configuration has also been established in 131Xe. The MR band has been interpreted in terms of shears mechanism with principal axis cranking (SPAC) calculations. Shell Model calculations are carried out to describe the non yrast states of 131Xe above the 11/2− isomer. New excited states have also been identified in 130Xe, produced in the same reaction.

Effect of Wetting and Dewetting Dynamics on Atomic Force Microscopy Measurements

Water bridge dynamics between an atomic force microscopy (AFM) tip and a flat substrate is studied by using a multibody dissipative particle dynamics (MDPD) model. First, the numerical model is validated by comparing the present results of droplet contact angles and liquid bridges with those reported in the literature. Then, the ability of MDPD to capture the meniscus shape and behavior for different operating conditions and geometric parameters is examined for both static and dynamic cases. Hence, several parametric studies and analyses of the AFM tip configuration and its operating conditions are reported. It is found that a critical capillary number of about 0.001 is calculated based on 5% change on the force measurements between the static and dynamic results. It is also demonstrated that the hysteresis behavior in the capillary force exerted on the AFM tip can be successfully predicted by using the MDPD model when the tip approaches or retracts from the substrate. Moreover, there is an excellent agreement in the results of breakup distance for different water bridge volumes between the predictions of the MDPD model and the theory. Also, the hysteresis of capillary force exerted on an AFM tip composed of multibody design is studied. The prediction on the transition of the capillary force vs distance between the AFM tip and the substrate is in good agreement with the experimental results. Therefore, we demonstrate a validated MDPD model which can successfully capture liquid bridge dynamics. This model can be used as a powerful design tool for meniscus manipulation technology, such as dip-pen nanolithography, as well as for studying dynamic, e.g., tapping mode AFM tip, interactions with a liquid bridge.

Depolarizing-Field Effects in Epitaxial Capacitor Heterostructures

We identify a transient enhancement of the depolarizing field, leading to an unexpected quench of net polarization, during the growth of a prototypical metal-ferroelectric-metal epitaxial system made of BaTiO_{3} and SrRuO_{3}. Reduced conductivity and, hence, charge screening efficiency in the early growth stage of the SrRuO_{3} top electrode promotes a breakdown of ferroelectric BaTiO_{3} into domains. We demonstrate how a thermal annealing procedure can recover the single-domain state. By tracking the polarization state in situ, using optical second harmonic generation, we bring new understanding to interface-related electrostatic effects in ferroelectric capacitors.

Neuronal clusterin expression is associated with cognitive protection in amyotrophic lateral sclerosis

AIMS

Clusterin is a topologically dynamic chaperone protein with the ability to participate in both intra- and extacellular proteostasis. Clusterin has been shown to be upregulated in the spinal cord of patients with amyotrophic lateral sclerosis (ALS) and has been shown to protect against TDP-43 protein misfolding in animal and cell models. Previous studies have demonstrated an association between the pathological burden of TDP-43 misfolding and cognitive deficits in ALS, demonstrating high specificity, but correspondingly low sensitivity owing to a subset of individuals with no evidence of cognitive deficits despite a high burden of TDP-43 pathology, called mismatch cases.

METHODS

Hypothesizing that differences in the ability to cope with protein misfolding in these cases may be due to differences in expression of protective mechanisms such as clusterin expression, we assessed the spatial expression of clusterin and another chaperone protein, HspB8, in post mortem brain tissue of mismatch cases. We employed a modified in situ hybridization technique called BaseScope, with single cell, single transcript resolution.

RESULTS

Mismatch cases demonstrated differential spatial expression of clusterin, with a predominantly neuronal pattern, compared to cases with cognitive manifestations of their TDP-43 pathology who demonstrated a predominantly glial distribution of expression.

CONCLUSIONS

Our data suggest that, in individuals with TDP-43 pathology, predominantly neuronal expression of clusterin in extra-motor brain regions may indicate a cell protective mechanism delaying clinical manifestations such as cognitive dysfunction.

Fermi Volume Evolution and Crystal-Field Excitations in Heavy-Fermion Compounds Probed by Time-Domain Terahertz Spectroscopy

We measure the quasiparticle weight in the heavy-fermion compound CeCu_{6-x}Au_{x} (x=0, 0.1) by time-resolved terahertz spectroscopy for temperatures from 2 up to 300 K. This method distinguishes contributions from the heavy Kondo band and from the crystal-electric-field satellite bands by different terahertz response delay times. We find that the formation of heavy bands is controlled by an exponentially enhanced, high-energy Kondo scale once the crystal-electric-field states become thermally occupied. We corroborate these observations by temperature-dependent dynamical mean-field calculations for the multiorbital Anderson lattice model and discuss consequences for quantum-critical scenarios.