Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Studies of Phospho-MurNAc-pentapeptide Translocase and Ternary Complex of a NaV C-Terminal Domain, a Fibroblast Growth Factor Homologous Factor, and Calmodulin

Phospho-MurNAc-pentapeptide translocase (MraY) is a conserved membrane-spanning enzyme involved in the biosynthesis of bacterial cell walls. MraY generates lipid I by transferring the phospho-MurNAc-pentapeptide to the lipid carrier undecaprenyl-phosphate. MraY is a primary target for antibiotic development because it is essential in peptidoglycan synthesis and targeted by 5 classes of natural product antibiotics. The structure of this enzyme will provide insight into the catalytic mechanism as well as a platform for future antibiotic development. MraY genes from 19 bacteria were cloned, expressed, purified and assayed for biochemical stability. The initial crystallization screening revealed that MraY from Aquifex aeolicus (MraY AA) produced diffracting crystals. Recombinant MraY AA is functional and shows inhibition by the natural inhibitor capuramycin. After extensive optimization of crystallization conditions, the resolution limit of the crystal was extended to 3.3 Å. The crystal structure presented here is the first structure of a member of the polyprenyl-phosphate N-acetyl hexosamine 1-phosphate transferase (PNPT) superfamily. This structure together with our functional dataallows us to identify the location of Mg 2+ at the active site and the putative binding sites of both substrates. My crystallographic studies provide insights into the mechanism of how MraY attaches a building block of peptidoglycan to the carrier lipid. Voltage-gated Na + (Na V) channels initiate action potentials in neurons and cardiac myocytes. Na V channels are composed of a transmembrane domain responsible for voltage-dependent Na + conduction and a cytosolic C-terminal domain (CTD) that iv regulates channel function through interactions with many auxiliary proteins including members of the fibroblast growth factor homologous factor (FHF) family and calmodulin (CaM). Incollaboration withGeoffrey Pitt's lab, we report the first crystal structure of the ternary complex of the human Na V 1.5 CTD, FGF13, and Ca 2+-free CaM at 2.2 Å. Combined with functional experiments based on structural insights, we present a platform to understand the roles of these auxiliary proteins in Na V channel regulation and the molecular basis of mutations that lead to neuronal and cardiac diseases. Furthermore, we identify a critical interaction that contributes to the specificity between individual Na V CTD isoforms and distinctive FHFs.
Prescribing Pattern of Anti-Hypertensive Drugs and Adherence to JNC VII Guideline

Introduction: Hypertension is an important public health concern because of its associated morbidity, mortality and economic impact on society. It is a significant risk factor for cardiovascular, cerebrovascular and renal complications. A number of national and international guidelines for the management of hypertension have been published. The Joint National Committee (JNC) in 2003 published a series of guidelines to recommend the appropriate antihypertensive therapy based on the best available evidence. Objectives: This drug utilization study was intended to find out the preferred drug group prescribed either alone or in combinations and their adherence to the JNC 7 guidelines. Materials and Methods: This was a prospective cross-sectional study. Drug utilization data on 100 hypertensive patients were collected from various hospitals in Nepal. The patients who received antihypertensive drugs during their treatment period in SPSS V. 16.0. The prescribed drugs were compared with JNC 7 guidelines. Results: It was found that 40% of patients were male and 60% were female. The largest subset of female hypertensive patients (45.0%) were in the age group of >60 years and a plurality of male hypertensive patients (45.0%) were in the age group of 40–60 years. It was found that 45% of the patients had Stage 1 hypertension, 32% of the patients were in prehypertension, 17% of the patients had Stage 2 hypertension. The most frequently prescribed antihypertensive drug regimens were angiotensin receptor blockers (ARBs) (32.44%), ARB + thiazide (15.94%), diuretics (11.59%), calcium channel blockers (CCBs) + beta blockers (9.42%) and CCBs (8.7%). Thirty-nine percent received monotherapy while the remaining 61% received combination therapy. Seventy-four percent of the total prescriptions followed JNC 7 guidelines. Conclusion: There is a need to follow official guidelines in managing hypertension as a chronic disease, since these guidelines are based on various clinical trials, and the successful attainment of a target BP in patients will be made much easier by implementing them. National health policymakers should consider the evaluation and treatment of hypertension as a right in the public health system for better outcomes in terms of morbidity and mortality from hypertension.
Tele-Oncology: A Validation Study of Choroidal and Iris Nevi

Background/Aims: To evaluate teleophthalmological assessment of choroidal and iris nevi (tele-oncology) compared to traditional in-person clinical evaluation for detection of either axial or basal growth. Methods: This is a validation study. All 97 eyes of 99 patients were evaluated with an in-person ocular oncology visit utilizing standard testing, and subsequently had a tele-oncology evaluation with the standardized tests. The tele-oncology reviewer was blinded to the in-person examination findings. The primary study outcome was detection of nevus growth on tele-oncology compared to in-person clinical examination. Results: Patients had a mean age of 61 years and the majority had nevi located in the choroid (n = 87; 88%). The most common diagnosis was a low-risk nevus (n = 38; 44%). By tele-oncology assessment, 11 eyes showed growth. Ten of these patients had growth confirmed on in-person clinical examination. Resultantly, tele-oncology assessment of choroidal and iris nevi growth had a sensitivity of 100%, specificity of 99%, positive predictive value (PPV) of 91%, and negative predictive value (NPV) of 100%. Conclusions: The results of this study suggest that tele-oncology is a safe platform for monitoring choroidal and iris nevi for growth, with excellent sensitivity, specificity, PPV, and NPV.
Characterisation of genetic complexity in chronic lymphocytic leukaemia

I ACKNOWLEDGEMENTS . V INDIVIDUAL CONTRIBUTIONS . VII PUBLICATIONS ARISING FROM THIS WORK . IX CONTENTS . XI LIST OF FIGURES . XIX LIST OF TABLES . XXI LIST OF ABBREVIATIONS . XXIII CHAPTER
Workforce Perceptions of Hospital Safety Culture at One Governmental Hospital in Alexandria

Background: Safety culture is increasingly recognized as an important strategy to improve patient safety. Objectives: The present study aimed at assessing workforce perception of hospital safety culture at Shark El Madina hospital and to identify differences in perception of safety culture dimensions among different professional categories at the study hospital. Methods: The study utilized a self administered questionnaire titled “Patient Safety Climate in Health Care Organizations” (PSCHO) which is composed of 38 items. A total of 186 completed questionnaires were collected distributed among 64 physicians, 74 nurses and 48 technicians. The mean score of items and dimensions were calculated as well as the percent problematic response (PPR) which is the fraction of survey participants who answered in ways that are inconsistent with an optimal safety culture. Results: The study revealed that the overall PPR was 46.9%, being highest among nurses (53.1%) %), followed by physicians (44.3%) and lowest among technicians (39.5%). Nurses had higher percentage of PPR than other professional groups in 8 dimensions. The 3 dimensions which had the lowest mean scores among the three professional categories were fear of blame followed by unit recognition and support for safety followed by organizational resources for patient safety. Nurses showed lower mean scores in five out of nine safety culture dimensions. Conclusion and Recommendations: Patient safety culture among health care workers at Shark El Madina hospital is relatively negative. There are differences among professional categories with nurses showing more negative view of safety culture dimensions. It is recommended to establish safety cultural change through education and training of staff, encouragement of no blame environment and provision of resources for patient safety.
A new mouse model for noninvasive fluorescence‐based monitoring of mitochondrial UCP1 expression

Mitochondrial uncoupling protein 1 (UCP1) is well known for its thermogenic function in brown adipose tissue (BAT). Since UCP1 expends energy on thermogenesis, UCP1 activation has been considered an approach to ameliorate obesity. As a tool for uncovering yet unknown mechanisms of UCP1 activation, we generated a transgenic mouse model in which UCP1 expression levels are reflected in fluorescence derived from monomeric red fluorescent protein 1 (mRFP1). In these UCP1‐mRFP1 BAC transgenic mice, fluorescence intensity mimics the change in UCP1 expression levels evoked through physiological or pharmacological stimulation. This transgenic mouse model will be useful in the search for bioactive compounds with the ability to induce UCP1 and for revealing undiscovered mechanisms of BAT activation.
Age-Period-Cohort Models

Outcomes of interest often depend on the age, period, or cohort of the individual observed, where cohort and age add up to period. An example is consumption: consumption patterns change over the lifecycle (age) but are also affected by the availability of products at different times (period) and by birth-cohort-specific habits and preferences (cohort). Age-period-cohort (APC) models are additive models where the predictor is a sum of three time effects, which are functions of age, period, and cohort, respectively. Variations of these models are available for data aggregated over age, period, and cohort, and for data drawn from repeated cross-sections, where the time effects can be combined with individual covariates. The age, period, and cohort time effects are intertwined. Inclusion of an indicator variable for each level of age, period, and cohort results in perfect collinearity, which is referred to as “the age-period-cohort identification problem. ” Estimation can be done by dropping some indicator variables. However, dropping indicators has adverse consequences such as the time effects are not individually interpretable and inference becomes complicated. These consequences are avoided by instead decomposing the time effects into linear and non-linear components and noting that the identification problem relates to the linear components, whereas the non-linear components are identifiable. Thus, confusion is avoided by keeping the identifiable non-linear components of the time effects and the unidentifiable linear components apart. A variety of hypotheses of practical interest can be expressed in terms of the non-linear components.
e-vaccination:Fingerprint Based Vaccination Monitoring System

- Immunization against common childhood diseases has been an integral part of mother and child health services in India. In developing countries, current vaccination status ofinfants is recorded ina paper, which is ineffective in many ways:information which may go missing, process of looking up data is tedious. The main objective of proposed work is to use biometric traits (fingerprint) of an infant to store their vaccination schedule details,thereby automating the vaccination schedule for the infant.Biometrics traits are usedsince fingerprint of infants have great potential to accurately record immunizations and helps greatly in efficiently searching the data. The proposed method aims at developing an application which provides to alerts on a regular basis toparents and Accredited Social Health Activist (ASHA) workers based on the stored vaccination schedule information.
The Molecular Detection of HPV Infection in samples of Iraqi Women with Abnormal cervical Smears

Human papillomavirus (HPV) types 16 and 18 cause almost 70% of cervical cancer cases worldwide. Recently, testing for high-risk HPV types have been adopted by clinical practices for the early detection of cervical cancer in conjunction with cytology tests. Cervical swab samples were collected at the Outpatient Gynecology department of Baghdad Teaching Hospital. These samples consisted of a patient group of 50 samples, and a healthy control group of 10 samples. A papanicolaou test (abbreviated as a Pap test) was also performed for each woman to examine the epithelial cells of both the endocervix and the upper vaginal region. Total DNA (genomic, mitochondrial, and viral) was extracted from cervical swab samples for molecular studies. HPV DNA testing was first done by using Real-Time PCR technology to target the L1 region of HR-HPV with specifically designed primers. This was followed by using AmpliSens kit for specific detection and genotyping of HPV16 and 18 with multiplex Real-Time PCR. The results of RT-PCR detection revealed that out of 16 samples detected with high-risk HPV, 5 samples were shown to be infected with HPV-16 and 5 samples were shown to be infected with HPV-18. These results show a significant relationship between the histological outcome of the patient and persistent HPV infection.
Does pembrolizumab have an effect on prolonging overall survival in patients with non-small cell lung cancer expressing programmed death ligand-1 (PD-L1)?

Objective: The objective of this selective EBM review is to determine whether or not pembrolizumab has an effect on prolonging overall survival in patients with non-small cell lung cancer expressing programmed death ligand-1 (PD-L1). Study Design: Review of two randomized controlled trials and one cohort study published in English in peer review journals. Data Sources: Two randomized controlled trials and one cohort study, which evaluated the efficacy of pembrolizumab on non-small cell lung cancer with PD-L1 expression compared to chemotherapy. All studies were found in PubMed database. Outcomes Measured: Overall survival measured by Kaplan-Meier analysis of overall survival. Results: Both of the RCT (Reck 2016 and Herbst 2016) showed pembrolizumab to be statistically effective in prolonging overall survival in patients with NSCLC expressing PD-L1 (p=0.005 and p<0.0001 respectively). Both studies showed a higher increase in overall survival in patients treated with pembrolizumab compared to those treated with traditional chemotherapy. In the cohort study conducted by Goldberg (2016), overall survival was measured to be 7.7 months (95% CI). Pembrolizumab also showed to have a positive effect on brain metastases as well. Conclusions: All studies included in this systematic review indicate that pembrolizumab is effective in prolonging overall survival in patients with NSCLC expressing PD-L1.
Coronavirus Disease-19: Summary of 2,370 Contact Investigations of the First 30 Cases in the Republic of Korea

Between January 24 and March 10, of a total of 2,370 individuals who had contacted the first 30 cases of COVID19, 13 were found to have COVID19, resulting secondary attack rate of 0.55% (95% CI 0.31 to 0.96). Of 119 household contacts, 9 had infections resulting secondary attack rate of 7.56 (95% CI 3.73 to 14.26).
Effect of seed size and color on germination of Cecropia obtusifolia Bertol (Cecropiaceae)

Se estudió el efecto de tamaño y color de la semilla de Cecropia obtusifolia Bertol en su germinación. Hubo dos tamaños: semillas chicas (1.3 mm longitud) y grandes (1.7 mm longitud); tres colores de la cubierta seminal: negro, café claro y café oscuro; dos temperaturas en cámara de ambiente controlado: 30 °C en el día y 25 °C en la noche, 25 °C en el día y 20 °C en la noche. El diseño experimental fue de bloques completos al azar, con los bloques anidados dentro del factor temperatura. El color y el tamaño influyeron significativamente (p≤0.05) en la capacidad germinativa, al igual que las interacciones temperatura×color, tamaño×color, y la interacción triple: temperatura×tamaño× color. Las semillas grandes germinaron casi el doble que las pequeñas; las de color café oscuro germinaron bien en ambos regímenes de temperatura. Con temperatura alta la mayor germinación fue en semillas grandes color café claro; con temperatura baja, las semillas grandes color café oscuro germinaron más. Así, las variantes en tamaño y color de las semillas les permiten germinar en distintas condiciones ambientales.
Compatibility of antagonists with Azospirillum in sesamum

A pot culture experiment was conducted to test the compatibility of antagonists, (Trichoderma, Gliocladium and Bacillus with Azospirillum) against root rot (caused by Macrophomina phaseolina) in a sesame crop. A combination of antagonists along with Azospirillum increased the root and shoot length of sesame significantly compared with Azospirillum alone. Reduced root rot and increased rhizosphere population were found in combined applications of antagonists. A combined application of all 3 antagonists resulted in the lowest root rot (13.3%) and increased shoot and root length. The rhizosphere population of Trichoderma and Gliocladium was reduced when applied with Bacillus subtilis.
Eurythermalism of a deep-sea symbiosis system from an enzymological aspect

III PREFACE. V ACKNOWLEDGEMENT. VII ABBREVIATIONS.XIX CHAPTER ONE – INTRODUCTION AND LITERATURE REVIEWS. 1 I. A REVIEW OF THE ‘EQUILIBRIUM MODEL’ . 3 a. State of the Field prior to the Equilibrium Model . 3 Enzyme “Temperature Optima” . 5 Does Stability Equate to Activity? 8 b. The Foundation of the Equilibrium Model . 9 The Active-Inactive Equilibrium . 9 c. The Structural Basis of the Eact–Einact Equilibrium . 12 d. The Implications of Parameters Derived from the Equilibrium Model . 14 II. TEMPERATURE ADAPTATION AND EURYTHERMALISM . 15 a. The Challenges of Temperature Adaptation. 16 Three Ways to Skin a Cat . 17 One More Way to Skin a Cat . 19 b. Enzymes from Extremophiles. 20 Psychrophiles.20 Hyperthermophiles . 21 III. ALVINELLA POMPEJANA AND ITS EPISYMBIONTS . 23
Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.
Produtividade e qualidade de gentipos de melo-amarelo em quatro ambientes

With the objective of identify genotypes of yellow melon export type and with high yield, were evaluated nine genotypes in four environments in Potiguar West. The experiments were established in the Mossoro-Assu Agricultural Pole, Rio Grande do Norte State - Brazil. The experimental design was in randomized blocks with four replications and 16 plants for plot. The genotypes evaluated were: Rochedo, TSX-32096; PX 4910606, Gold Mine, PX-1010606; Yellow Queen; Gold Pride; Yellow King; AF-646 and AF-682. The genotypes that presented higher total productivity were TSX-32096, Gold Mine, PX-4010606, Yellow Queen and Gold Pride, with average of 55.1 t/ha, and with higher marketable productivity were TSX-32096, Rochedo, Gold Mine, PX-4010606 and Gold Pride in Mossoro (40.1 t/ha) and Carnaubais (46.2 t/ha), and the genotypes AF-646, Yellow Queen and AF-682 in Barauna (63.1 t/ha), this environment provided the largest marketable productivity, overcoming in 53%, 75% and 166% the environments of Carnaubais, Mossoro and Alto do Rodrigues. The fruit mean weight was influenced by the cultivation environment, ranging from 1.07 kg in Mossoro to 1.64 kg in Barauna. The higher concentration of soluble solids was verified in the genotypes AF-646 (11.1%), PX-4910606 (11.0%), Yellow King (10.7%) and TSX-32096 (11.3%).
Genetic bottleneck studies in five duck (Anas platyrhynchos) populations of India.

The data of 24 microsatellite loci were generated for 4 indigenous duck populations and 1 commercial breed (Khakhi Campbell). The data were subjected to statistical analysis to test for heterozygosity excess or deficiency since any bottlenecked population would undergo transient heterozygosity excess. Three tests, viz. Sign-rank test, Standardised differences test and Wilcoxon test were utilised in each of the three models of mutations, IAM, SMM and TPM. SMM, which is the most suited model for evolution of microsatellites did not reveal any bottleneck in the last few generations. In our present study the heterozygosity excess is not evident in any of the 5 duck populations and thus the duck populations of India under study are in mutation drift equilibrium. The rejection of null hypothesis in the duck populations is attributed to heterozygotic deficiency.
"It’s about a restricted living environment": Experiences in supported housing of people who use forensic mental health services

"It’s about a restricted living environment": Experiences in supported housing of people who use forensic mental health services By Marlee Jordan The forensic mental health population is made up of individuals who are living with mental illness and encounter the criminal justice system. Supported housing—which combines housing and mental health support and services—as part of the larger forensic system must manage individuals’ risk to ensure public safety, and attend to the rehabilitative needs of forensic mental health populations. Drawing on ‘therapeutic surveillance’, my study explored experiences in supported housing of people found Not Criminally Responsible on account of Mental Disorder. Photovoice and in-depth interviews were conducted with three individuals living in supported housing. Data were analyzed inductively using thematic analysis and produced three overarching themes, including ‘It feels like a normal house’, ‘Being responsible, being able to live independently’, and ‘Parts of it are a very restricted living environment’. The results point to the ways in which supported housing was experienced as empowering, and, at times, restrictive and controlling.