Clinical and laboratory predictors of 30-day mortality in severe acute malnourished children with severe pneumonia

OBJECTIVE

To determine the predictors of mortality within 30 days of hospital admission in a diarrhoeal disease hospital in Bangladesh.

METHODS

Cohort study of hospitalised children aged 0-59 months with severe acute malnutrition (SAM) and severe pneumonia in Dhaka Hospital, icddr,b, Bangladesh from April 2015 to March 2017. Those discharged were followed up, and survival status at 30 days from admission was determined. Children who died were compared with the survivors in terms of clinical and laboratory biomarkers. Multivariable logistic regression analysis was used for calculating adjusted odds ratio for death within 30 days of hospital admission.

RESULTS

We enrolled 191 children. Mortality within 30 days of admission was 6% (14/191). After adjusting for potential confounders (hypoxia, CRP and haematocrit) in logistic regression analysis, independent factors associated with death were female sex (aOR = 5.80, 95% CI: 1.34-25.19), LAZ <-4 (aOR = 6.51, 95% CI: 1.49-28.44) and Polymorphonuclear Leucocytes (PMNL) (>6.0 × 10⁹ /L) (aOR = 1.06, 95% CI: 1.01-1.11). Using sex, Z-score for length for age (LAZ), and PMNL percentage, we used random forest and linear regression models to achieve a cross-validated AUC of 0.83 (95% CI: 0.82, 0.84) for prediction of 30-day mortality.

CONCLUSIONS

The results of our data suggest that female sex, severe malnutrition (<-4 LAZ) and higher PMNL percentage were prone to be associated with 30-day mortality in children with severe pneumonia. Association of these factors may be used in clinical decision support for prompt identification and appropriate management for prevention of mortality in this population.

Using patient–centered approach for improving adherence to treatment in DS/DR–TB patients in Ukraine

Issue/problem

Ukraine is among 30 high MDR-TB burden countries with about 6500 laboratory confirmed MDR-TB cases annually. Ukraine provides full coverage for first- and second-line TB drugs from the state budget. Nevertheless, successful treatment outcomes are one of the lowest in EECA region - 49% in MDR/RR-TB cases and 37% in XDR-TB. High rates of lost to follow-up (15.8%), treatment failed (18%) and died (15.9%) among MDR-TB cases contribute to unsuccessful treatment outcomes.

Description of the problem

A new intervention was introduced aimed at improving patients' adherence to treatment. Medical-psycho-social services (MPSS) provision based on patient-centered approach is provided to all patients. In 2018, project funded by GFATM was launched in 8 oblasts of Ukraine. All patients are assessed on treatment adherence before discharge from hospitals. Those with low adherence are referred to NGOs. MPSS starts from the patient's needs assessment followed by development of individual plan of support. MPSS is provided during the whole period of outpatient treatment and may include DOT/VOT, social workers' permanent support, food kits, psychologist counselling, transport and/or cell reimbursement, housing, documents restore, legal services and other services as per patients' needs. Electronic depersonalized database SyrEx is used for the project related notes.

Results

Total amount of TB/DR-TB patients treated in 2018-2019 is 8640 and 4246 accordingly. Cohort analysis is used for treatment outcomes assessment.

Intervention allowed reducing the number of patients lost to follow up in DS/DR-TB (to 1.2% and 2.5% accordingly), treatment failed (to 5.4% and 10.9%) and number of died (to 2.1% and 3.2%)

Lessons

MPSS based on patient-centered approach improved successful treatment outcomes: to 91% in DS-TB patients and 82.3% in DR-TB. Further initiative scale-up is required as well as transition of MPSS services from donor funding to domestic.

Over-expression of Caj1, a plasma membrane associated J-domain protein in Saccharomyces cerevisiae, stabilizes amino acid permeases

Hsp70: J-domain protein (JDP) machines, along with the cellular protein degradation systems play a central role in regulating cellular proteostasis. An equally robust surveillance system operates at the plasma membrane too that affects proper sorting, stability as well as the turnover of membrane proteins. Although plausible, a definitive role of the Hsp70: JDP machine in regulating the stability of plasma membrane proteins is not well understood in Saccharomyces cerevisiae. Here we show that a moderate over-expression of Caj1, one of the thirteen JDPs residing in the nucleo-cytosolic compartment of S. cerevisiae reduced the cold sensitivity of tryptophan auxotrophic yeast cells by stabilizing tryptophan permeases, Tat1 and Tat2 in a J-domain dependent manner. Concomitantly, higher Caj1 levels also caused slow growth and increased plasma membrane damage at elevated temperatures possibly due to the stabilization of thermolabile plasma membrane proteins. Finally, we show that although majorly cytosolic, Caj1 also co-localizes with the membrane dye FM4-64 at the cellular periphery suggesting that Caj1 might interact with the plasma membrane. Based on the results presented in this study, we implicate the Hsp70: Caj1 chaperone machine in regulating the stability or turnover of plasma membrane proteins in budding yeast.

Validated Instruments of Quality of Life (QOL) in Patients With Acute Myeloid Leukemia (AML) and Other Cancers

Introduction

Acute myeloid leukemia (AML) can negatively impact quality of life (QOL). Few QOL instruments are specific to and have been validated in AML. This review aims to identify QOL instruments that have been validated in patients with AML and other cancers and summarize their psychometric properties reported in published literature. A literature review search was performed using PubMed and OVID (Biosis, Embase, MEDLINE) databases through June 25, 2020. Search terms included: QOL, health-related QOL, patient-reported outcomes and validity, reliability, validated, tools, instruments, test-retest, and leukemia myeloid acute, leukemia, myeloid, acute, acute myeloid leukemia. Articles were included if they focused on cancer and reported psychometric properties that could be extracted. Abstracts and their references were reviewed for inclusion.

Results

Twelve evaluating ten instruments were included. Functional Assessment of Cancer Therapy Leukemia (FACT-Leu) showed internal consistency (IC) of α = 0.86 to >0.9, correlation with EQ-5D-3L of r > 0.50, correlation with European Organisation for Research and Treatment of Cancer (EORTC) QLQ-Leu of ρ = 0.29–0.63, test-retest reliability of κ = 0.861. FACT-F showed correlations with EORTC QLQ-C30 of r = 0.40–0.83. Hematological Malignancy Patient-Reported Outcome (HM-PRO) showed intraclass correlation coefficient (ICC) of 0.94–0.98. EORTC-8D and EQ-5D-3L showed ICC = 0.595, correlations with each other of ρ = 0.137–0.634 and with EORTC QLQ-C30 of r = 0.651–0.917. EORTC QLQ-C30 showed person separation reliability of 0.47 to 0.90 and patient-observer agreement of 0.85. Life Ingredient Profile (LIP) showed IC of α = 0.29–0.77 and test-retest reliability of κ = 0.42–1.0. QOL-E showed correlation with FACT-general of R = 0.71, internal validity of α = 0.7, and test-retest reliability of standardized Cronbach’s α = 0.7–0.92. EORTC QLQ-Leu showed IC of α = 0.6–0.79. The Acute Myeloid Leukemia–Quality of Life (AML-QOL) instrument showed IC of α = 0.72, correlations with EORTC QLQ-30 of magnitudes ρ = 0.59–0.72, and test-retest reliability of ICC = 0.52–0.91.

Conclusion

Although several QOL instruments have been validated, more research is needed to determine the most clinically useful instruments in patients with AML.

Evaluation of patient and healthcare provider (HCP) knowledge, attitudes, and behavior for safety and use of pexidartinib

e23580

Background: Pexidartinib, a kinase inhibitor, is approved for treatment of adult patients with symptomatic tenosynovial giant cell tumor (TGCT) associated with severe morbidity or functional limitations and not amenable to improvement with surgery. Due to risk of serious and potentially fatal liver injury, pexidartinib is available via a Risk Evaluation and Mitigation Strategy (REMS) Program. A requirement of the REMS is to conduct a qualitative evaluation of stakeholder Knowledge, Attitudes, and Behavior (KAB) of risks via surveys. The objective of the qualitative evaluation is to review key risk message questions with respect to understanding, relevance, clarity and provide recommendations on alternative language, phrasing, and structure. Methods: Anonymized, one-on-one 45–60-min phone interviews with patients and HCPs were conducted by UBC. Patients ≥18 y, diagnosed with TGCT (prioritized) or metastasis/sarcoma of the connective tissue, with different levels of education and fluent reading/speaking English were included. To participate, HCPs were required to treat patients with TGCT (prioritized) or metastasis/sarcoma of the connective tissue, treat patients ≥75% of their time, and clearly read/speak English. Participants were required to complete an Interview Release Form (IRF) and confirm access to a computer/tablet. Participants had little/no familiarity with pexidartinib materials. All interviews followed a standard process, used a pre-scripted guide on general instructions, confidentiality, safety event reporting, rapport building and assessment of health literacy (patients only). Feedback regarding understanding, relevance, and clarity were used to recommend potential alternate language/phrasing. To receive compensation participants were required to execute/return the IRF. Results: Twelve patients were interviewed, majority 67% had TGCT; mean age 52 y; 58% female; 42% reported some college/associates degree. 12 HCPs were interviewed, 67% treated patients with TGCT; 100% male; mean years practicing 22; all spent 75% or more time seeing patients; primary specialty Orthopedics. Areas of confusion/misunderstanding were reported, and questions were then revised. Patient findings: complexity and wordiness; HCP findings: repetition/difficulty reading, and some terminology was not self-explanatory. Conclusions: Feedback from HCPs and patients was received to improve the key risk messages of the KAB. Qualitative research is recommended to improve comprehension and data quality collected.

Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase

Thymidylate synthase (TSase), an enzyme responsible for the de novo biosynthesis of 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) necessary for DNA synthesis, has been a drug target for decades. TSase is a highly conserved enzyme across species ranging from very primitive organisms to mammals. Among the many conserved active site residues, an asparagine (N177, using Escherichia coli residues numbering) appears to make direct hydrogen bonds with both the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate and its pyrimidine ring's N3. Recent studies have reassessed the TSase catalytic mechanism, focusing on the degree of negative charge accumulation at the O4 carbonyl of the substrate during two critical H-transfers - a proton abstraction and a hydride transfer. To obtain insights into the role of this conserved N177 on the hydride transfer, we examined its aspartic acid (D) and serine (S) mutants - each of which is expected to alter hydrogen bonding and charge stabilization around the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate. Steady-state kinetics, substrate binding order studies and temperature-dependency analysis of intrinsic KIEs for the hydride transfer step of the TSase catalytic cycle suggest the active site of N177D is not precisely organized for that step. A smaller disruption was observed for N177S, which could be rationalized by partial compensation by water molecules and rearrangement of other residues toward preparation of the system for the hydride transfer under study. These experimental findings are qualitatively mirrored by QM/MM computational simulations, thereby shedding light on the sequence and synchronicity of steps in the TSase-catalyzed reaction. This information could potentially inform the design of mechanism-based drugs targeting this enzyme.

Quantitative Characterization of the Nanoscale Local Lattice Strain Induced by Sr Dopants in La_{1.92}Sr_{0.08}CuO_{4}

The nanometer scale lattice deformation brought about by the dopants in the high temperature superconducting cuprate La_{2-x}Sr_{x}CuO_{4} (x=0.08) was investigated by measuring the associated x-ray diffuse scattering around multiple Bragg peaks. A characteristic diffuse scattering pattern was observed, which can be well described by continuum elastic theory. With the fitted dipole force parameters, the acoustic-type lattice deformation pattern was reconstructed and found to be of similar size to lattice thermal vibration at 7 K. Our results address the long-term concern of dopant introduced local lattice inhomogeneity, and show that the associated nanometer scale lattice deformation is marginal and cannot, alone, be responsible for the patched variation in the spectral gaps observed with scanning tunneling microscopy in the cuprates.

Capsular genotype and lipooligosaccharide locus class distribution in Campylobacter jejuni from young children with diarrhea and asymptomatic carriers in Bangladesh

Campylobacter jejuni-related diarrheal diseases is one of the major health issues among young children (0-59 months old) in low-income countries. Monitoring of the capsular (capsule polysaccharide, CPS) types of virulent C. jejuni strains in regions where the disease is endemic is of great importance for the development of a customized capsule-based multivalent vaccine. Therefore, we aimed to determine the prevalence of CPS genotypes among C. jejuni strains isolated from young children with enteritis (n = 152) and asymptomatic carriers matched by age, sex, and residence defined as the control group (n = 215) in Bangladesh. CPS genotyping was performed using a newly established multiplex polymerase chain reaction (PCR) method and lipooligosaccharide (LOS) locus classes (A-E) were characterized using PCR as well. We identified 24 different CPS genotypes among the 367 isolates. Four prevalent capsular types, HS5/31 complex (n = 27, 18%), HS3 (n = 26, 17%), HS4A (n = 10, 7%), and HS8/17 (n = 10, 7%) covered almost 50% of the strains from enteritis patients and 43% of the isolates from controls. In combination, the CPS genotype and LOS class was not discriminative between cases and controls. Dominant capsular types previously identified in C. jejuni strains isolated from patients with Guillain-Barré syndrome in Bangladesh were rarely detected in strains isolated from the young children. A similar distribution was evident among enteritis- and control-related strains when comparison was done between CPS types and LOS classes. This is the first systematic study presenting the distribution of CPS genotypes of C. jejuni strains isolated in Bangladesh from children with diarrhea and controls, with capsular genotypes HS5/31 complex, HS3, HS4A, and HS8/17 being prevalent in both. In conclusion, systematic studies are required to develop a multivalent capsule-based vaccine for children in low-income countries.

Nanocalorimeter platform for in situ specific heat measurements and x-ray diffraction at low temperature

Recent advances in electronics and nanofabrication have enabled membrane-based nanocalorimetry for measurements of the specific heat of microgram-sized samples. We have integrated a nanocalorimeter platform into a 4.5 T split-pair vertical-field magnet to allow for the simultaneous measurement of the specific heat and x-ray scattering in magnetic fields and at temperatures as low as 4 K. This multi-modal approach empowers researchers to directly correlate scattering experiments with insights from thermodynamic properties including structural, electronic, orbital, and magnetic phase transitions. The use of a nanocalorimeter sample platform enables numerous technical advantages: precise measurement and control of the sample temperature, quantification of beam heating effects, fast and precise positioning of the sample in the x-ray beam, and fast acquisition of x-ray scans over a wide temperature range without the need for time-consuming re-centering and re-alignment. Furthermore, on an YBa₂Cu₃O_7-δ crystal and a copper foil, we demonstrate a novel approach to x-ray absorption spectroscopy by monitoring the change in sample temperature as a function of incident photon energy. Finally, we illustrate the new insights that can be gained from in situ structural and thermodynamic measurements by investigating the superheated state occurring at the first-order magneto-elastic phase transition of Fe₂P, a material that is of interest for magnetocaloric applications.

Examinations of the Chemical Step in Enzyme Catalysis

Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions.

The general base in the thymidylate synthase catalyzed proton abstraction

The enzyme thymidylate synthase (TSase), an important chemotherapeutic drug target, catalyzes the formation of 2'-deoxythymidine-5'-monophosphate (dTMP), a precursor of one of the DNA building blocks. TSase catalyzes a multi-step mechanism that includes the abstraction of a proton from the C5 of the substrate 2'-deoxyuridine-5'-monophosphate (dUMP). Previous studies on ecTSase proposed that an active-site residue, Y94 serves the role of the general base abstracting this proton. However, since Y94 is neither very basic, nor connected to basic residues, nor located close enough to the pyrimidine proton to be abstracted, the actual identity of this base remains enigmatic. Based on crystal structures, an alternative hypothesis is that the nearest potential proton-acceptor of C5 of dUMP is a water molecule that is part of a hydrogen bond (H-bond) network comprised of several water molecules and several protein residues including H147, E58, N177, and Y94. Here, we examine the role of the residue Y94 in the proton abstraction step by removing its hydroxyl group (Y94F mutant). We investigated the effect of the mutation on the temperature dependence of intrinsic kinetic isotope effects (KIEs) and found that these KIEs are more temperature dependent than those of the wild-type enzyme (WT). These results suggest that the phenolic -OH of Y94 is a component of the transition state for the proton abstraction step. The findings further support the hypothesis that no single functional group is the general base, but a network of bases and hydroxyls (from water molecules and tyrosine) sharing H-bonds across the active site can serve the role of the general base to remove the pyrimidine proton.

Three-dimensional charge density wave order in YBa2Cu3O6.67 at high magnetic fields

Charge density wave (CDW) correlations have been shown to universally exist in cuprate superconductors. However, their nature at high fields inferred from nuclear magnetic resonance is distinct from that measured with x-ray scattering at zero and low fields. We combined a pulsed magnet with an x-ray free-electron laser to characterize the CDW in YBa2Cu3O6.67 via x-ray scattering in fields of up to 28 tesla. While the zero-field CDW order, which develops at temperatures below ~150 kelvin, is essentially two dimensional, at lower temperature and beyond 15 tesla, another three-dimensionally ordered CDW emerges. The field-induced CDW appears around the zero-field superconducting transition temperature; in contrast, the incommensurate in-plane ordering vector is field-independent. This implies that the two forms of CDW and high-temperature superconductivity are intimately linked.

Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction

Thymidylate synthase (TSase) catalyzes the de novo biosynthesis of thymidylate, a precursor for DNA, and is thus an important target for chemotherapeutics and antibiotics. Two sequential C-H bond cleavages catalyzed by TSase are of particular interest: a reversible proton abstraction from the 2'-deoxy-uridylate substrate, followed by an irreversible hydride transfer forming the thymidylate product. QM/MM calculations of the former predicted a mechanism where the abstraction of the proton leads to formation of a novel nucleotide-folate intermediate that is not covalently bound to the enzyme (Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A. Biochemistry2013, 52, 2348-2358). Existence of such intermediate would hold promise as a target for a new class of drugs. Calculations of the subsequent hydride transfer predicted a concerted H-transfer and elimination of the enzymatic cysteine (Kanaan, N.; Ferrer, S.; Marti, S.; Garcia-Viloca, M.; Kohen, A.; Moliner, V. J. Am. Chem. Soc.2011, 133, 6692-6702). A key to both C-H activations is a highly conserved arginine (R166) that stabilizes the transition state of both H-transfers. Here we test these predictions by studying the R166 to lysine mutant of E. coli TSase (R166K) using intrinsic kinetic isotope effects (KIEs) and their temperature dependence to assess effects of the mutation on both chemical steps. The findings confirmed the predictions made by the QM/MM calculations, implicate R166 as an integral component of both reaction coordinates, and thus provide critical support to the nucleotide-folate intermediate as a new target for rational drug design.

Campylobacter jejuni capsular genotypes are related to Guillain-Barré syndrome

In about one in a thousand cases, a Campylobacter jejuni infection results in the severe polyneuropathy Guillain-Barré syndrome (GBS). It is established that sialylated lipo-oligosaccharides (LOS) of C. jejuni are a crucial virulence factor in GBS development. Frequent detection of C. jejuni with sialylated LOS in stools derived from patients with uncomplicated enteritis implies that additional bacterial factors should be involved. To assess whether the polysaccharide capsule is a marker for GBS, the capsular genotypes of two geographically distinct GBS-associated C. jejuni strain collections and an uncomplicated enteritis control collection were determined. Capsular genotyping of C. jejuni strains from the Netherlands revealed that three capsular genotypes, HS1/44c, HS2 and HS4c, were dominant in GBS-associated strains and capsular types HS1/44c and HS4c were significantly associated with GBS (p 0.05 and p 0.01, respectively) when compared with uncomplicated enteritis. In a GBS-associated strain collection from Bangladesh, capsular types HS23/36c, HS19 and HS41 were most prevalent and the capsular types HS19 and HS41 were associated with GBS (p 0.008 and p 0.02, respectively). Next, specific combinations of the LOS class and capsular genotypes were identified that were related to the occurrence of GBS. Multilocus sequence typing revealed restricted genetic diversity for strain populations with the capsular types HS2, HS19 and HS41. We conclude that capsular types HS1/44c, HS2, HS4c, HS19, HS23/36c and HS41 are markers for GBS. Besides a crucial role for sialylated LOS of C. jejuni in GBS pathogenesis, the identified capsules may contribute to GBS susceptibility.

Concerted versus stepwise mechanism in thymidylate synthase

Thymidylate synthase (TSase) catalyzes the intracellular de novo formation of thymidylate (a DNA building block) in most living organisms, making it a common target for chemotherapeutic and antibiotic drugs. Two mechanisms have been proposed for the rate-limiting hydride transfer step in TSase catalysis: a stepwise mechanism in which the hydride transfer precedes the cleavage of the covalent bond between the enzymatic cysteine and the product and a mechanism where both happen concertedly. Striking similarities between the enzyme-bound enolate intermediates formed in the initial and final step of the reaction supported the first mechanism, while QM/MM calculations favored the concerted mechanism. Here, we experimentally test these two possibilities using secondary kinetic isotope effect (KIE), mutagenesis study, and primary KIEs. The findings support the concerted mechanism and demonstrate the critical role of an active site arginine in substrate binding, activation of enzymatic nucleophile, and the hydride transfer studied here. The elucidation of this reduction/substitution sheds light on the critical catalytic step in TSase and may aid future drug or biomimetic catalyst design.

Comparative population structure analysis of Campylobacter jejuni from human and poultry origin in Bangladesh

Campylobacter jejuni is the most important cause of antecedent infections leading to Guillain-Barré syndrome (GBS) and Miller Fisher syndrome (MFS). The objective of the present study was to define the genetic diversity, population structure, and potential role of poultry in the transmission of Campylobacter to humans in Bangladesh. We determined the population structure of C. jejuni isolated from poultry (n = 66) and patients with enteritis (n = 39) or GBS (n = 10). Lipooligosaccharide (LOS) typing showed that 50/66 (76 %) C. jejuni strains isolated from poultry could be assigned to one of five LOS locus classes (A-E). The distribution of neuropathy-associated LOS locus classes A, B, and C were 30/50 (60 %) among the typable strains isolated from poultry. The LOS locus classes A, B, and C were significantly associated with GBS and enteritis-related C. jejuni strains more than for the poultry strains [(31/38 (82 %) vs. 30/50 (60 %), p < 0.05]. Multilocus sequence typing (MLST) defined 15 sequence types (STs) and six clonal complexes (CCs) among poultry isolates, including one ST-3740 not previously documented. The most commonly identified type, ST-5 (13/66), in chicken was seen only once among human isolates (1/49) (p < 0.001). Amplified fragment length polymorphism (AFLP) revealed three major clusters (A, B, and C) among C. jejuni isolated from humans and poultry. There seems to be a lack of overlap between the major human and chicken clones, which suggests that there may be additional sources for campylobacteriosis other than poultry in Bangladesh.

Tuning magnetic coupling in Sr2IrO4 thin films with epitaxial strain

We report x-ray resonant magnetic scattering and resonant inelastic x-ray scattering studies of epitaxially strained Sr2IrO4 thin films. The films were grown on SrTiO3 and (LaAlO3)0.3(Sr2AlTaO6)0.7 substrates, under slight tensile and compressive strains, respectively. Although the films develop a magnetic structure reminiscent of bulk Sr2IrO4, the magnetic correlations are extremely anisotropic, with in-plane correlation lengths significantly longer than the out-of-plane correlation lengths. In addition, the compressive (tensile) strain serves to suppress (enhance) the magnetic ordering temperature TN, while raising (lowering) the energy of the zone-boundary magnon. Quantum chemical calculations show that the tuning of magnetic energy scales can be understood in terms of strain-induced changes in bond lengths.