Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical utility of targeted NGS panel with comprehensive bioinformatics analysis for patients with acute lymphoblastic leukemia

Abstract Acute lymphoblastic leukemia (ALL) is a genetically complex and heterogeneous disease for which a wide range of genetic variations has been identified. With the need for comprehensive high-throughput analysis, we have designed a comprehensive next-generation sequencing (NGS) assay to detect somatic mutations, translocations, and copy number changes and have evaluated its clinical utility in patients with ALL. The panel reliably detected single nucleotide variations (SNV) and copy number variations (CNV) analysis was exceptionally useful in identifying genic and chromosomal CNV which dominated the genetic abnormalities of ALL. We detected SNVs and CNVs simultaneously in a single assay, which could provide an alternative or supplement for several conventional tests and simplify the testing processes. We applied the genetic information obtained to the risk stratification of patients with high risk mutations and further confirmed the clinical utility of the comprehensive genetic testing with intensive bioinformatics analysis.
Optimizing Energy Expenditure and Oxygenation Toward Ventilator Tolerance is Associated with Lower Ventilator and ICU Days.

INTRODUCTION We hypothesize that if both energy expenditure and oxygenation are optimized (EEOO) towards ventilator tolerance; this would provide patients with the best condition to be liberated from the ventilator. We defined ventilator tolerance as having a RQ value between 0.7 and 1.0, while maintaining saturations above 98% with FiO2 70% or less and a normal respiratory rate without causing disturbances to the patient's pH. METHODS This is a single institution prospective cohort study of ventilator dependent patients within a closed trauma ICU. The study period was over 52 months. A total of 1,090 patients were part of the primary analysis. The test group (EEOO) was compared to a historical cohort, comparing 26 months in each study group. The primary outcome of this study was number of ventilator days. Secondary outcomes included in-hospital mortality, ICU LOS, overall hospital length of stay, tracheostomy rates, reintubation rates, and in hospital complication rates such as pneumonia and ARDS. Both descriptive and multivariable regression analysis were performed to compare the effects of the EEOO protocol to our standard protocols alone. RESULTS The primary outcome of number of ventilator days was significantly shorter the EEOO cohort by nearly 3 days. This was significant even after adjustment for age, gender, race, comorbidities, nutrition type, and injury severity, (4.3 vs. 7.2 days, pvalue 0.0001). The EEOO cohort also had significantly lower ICU days, hospital days, and overall complications rates. CONCLUSIONS Optimizing the patient's nutritional regimen to ventilator tolerance and optimizing oxygenation by means of targeted pulmonary mechanics and inspired FiO2 may be associated with lower ventilator and ICU days as well as overall complication rates. LEVEL OF EVIDENCE IV, comparative study.
An implementation of a word stemming algorithm for English

This short paper describes the implementation of a well-known suffix-stripping algorithm. This implementation is available under the latest version of the GNU public licence. 0.1 Overview In bibliographic indexing, it is very helpful if derivatives of words can be reduced to a common stem, for example, runs, running could both usefully be reduced to the stem run. For English, one of the standard ways of doing this is the algorithm described by [1]. This paper describes an implementation of this algorithm. 0.2 Implementation The algorithm is relatively complex and has been implemented as a C function for good performance. There are three source files in the package along with the infrastructure to repeat the regression tests. The files are:• stem proto.h: the interface prototype include file. • chance stem.c: the function wordStem() and some supporting functions. • test wordstem.c: a test harness for the function wordStem() • teststem.txt: a list of all the words and their stems from the original paper. • teststem.out: a regression output which should not be changed. • regress stem.sh: a Bourne shell script which makes and then runs the regression tests. • README STEM and COPYRIGHT files. The package contains around 800 lines of source code. 0.2. 1 Targets This package should run without change on Linux and Windows although it was developed under Linux. 0.2. 2 Running the regression tests Simply enter % regress_stem.sh This will make the package and run the regression test. It will report if any differences are found. It should be noted that the package correctly runs each section of the original paper [1] but in the paper, the examples were mostly for a single step of the algorithm. The output of the regression tests has all steps in the algorithm included. There are therefore minor changes from the list in the paper but these have been verified as being correct for the all step approach.
The Effect of High Intensity and Low Intensity Exercises on Body Fat and Weight Reduction

Previous studies have shown that long duration, Low Intensity (LI) exercise reduces weight and body fat percent, but the effect of short duration, High Intensity (HI) exercise is not clear. The purpose of this study was to compare the effect of LI exercise with HI exercise on Body Weight (BW) and Body Fat (BF) percent. Forty two male and female healthy college students have been randomly assigned to three different groups: LI, HI, none exercising (control) groups. The exercising groups underwent a supervised 14-week, 3 day/wk exercise program (LI group: 25 min of continuous run regardless of the intensity, HI group: 10 sec. max run, 10 sec. rest x 20 times). The results showed: a- BW loss and BF % reduction in both exercising groups but not in the control group is (P<0.01). b- None significant difference between both exercising groups. Conclusion: short duration bouts of a supervised HI exercise program in college aged males and females have similar beneficial effects on body composition and weight, as the effect of longer duration bouts of LI.
Antecedents and Consequences of Organizational Change: ‘Institutionalizing’ the Behavioral Theory of the Firm

In this paper, we highlight the conditions under which organizations initiate changes in two distinct institutional contexts. While the focus within behavioral research has been on aspiration-driven organizational change, the effect of institutional dynamics on the probability of change has been given limited attention. Pooled cross-sectional data covering the period 1920-2001 in the baseball industry are regressed to examine a set of hypotheses that predict the drivers of organizational change in periods of institutional stability and instability, as well as the impact of these changes on performance. Our findings show that the role of aspiration-driven organizational change diminishes in environments characterized by institutional instability. Rather, mimetic and cognitive pressures pave the ground for responses to institutional dynamics. We also shed light on how the relative stability/instability of the institutional environment heterogeneously influences the implications of behavioral changes for organizational performance.
Determinants of Interest Spread in Pakistan

Interest spread of the Pakistan’s banking industry has been on the rise for the last two years. The increase in interest spread discourages savings and investments on the one hand, and raises concerns on the effectiveness of bank lending channel of monetary policy on the other. This study examines the determinants of interest spread in Pakistan using panel data of 29 banks. The results show that inelasticity of deposit supply is a major determinant of interest spread whereas industry concentration has no significant influence on interest spread. One reason for inelasticity of deposits supply to the banks is the absence of alternate options for the savers. The on-going merger wave in the banking industry will further limit the options for the savers. Given the adverse implications of banking mergers for a competitive environment, we argue that to maintain a reasonably competitive environment, merger proposals may be subjected to review by an antitrust authority with the central bank retaining the veto over merger approval.
Detection of continuous variable entanglement without coherent local oscillators

We propose three criteria for identifying continuous variable entanglement between two many-particle systems with no restrictions on the quantum state of the local oscillators used in the measurements. Mistakenly asserting a coherent state for the local oscillator can lead to incorrectly identifying the presence of entanglement. We demonstrate this in simulations with 100 particles and also find that large number fluctuations do not prevent the observation of entanglement. Our results are important for quantum information experiments with realistic Bose-Einstein condensates or in optics with arbitrary photon states.
NEBULAR EXCITATION IN z ∼ 2 STAR-FORMING GALAXIES FROM THE SINS AND LUCI SURVEYS: THE INFLUENCE OF SHOCKS AND ACTIVE GALACTIC NUCLEI

Based on high-resolution, spatially resolved data of 10 z ∼ 2 star-forming galaxies from the SINS/zC-SINF survey and LUCI data for 12 additional galaxies, we probe the excitation properties of high-z galaxies and the impact of active galactic nuclei (AGNs), shocks, and photoionization. We explore how these spatially resolved line ratios can inform our interpretation of integrated emission line ratios obtained at high redshift. Many of our galaxies fall in the “composite” region of the z ∼ 0 [N ii]/Hα versus [O iii]/Hβ diagnostic (BPT) diagram, between star-forming galaxies and those with AGNs. Based on our resolved measurements, we find that some of these galaxies likely host an AGN, while others appear to be affected by the presence of shocks possibly caused by an outflow or from an enhanced ionization parameter as compared with H ii regions in normal, local star-forming galaxies. We find that the Mass-Excitation (MEx) diagnostic, which separates purely star-forming and AGN hosting local galaxies in the [O iii]/Hβ versus stellar mass plane, does not properly separate z ∼ 2 galaxies classified according to the BPT diagram. However, if we shift the galaxies based on the offset between the local and z ∼ 2 mass–metallicity relation (i.e., to the mass they would have at z ∼ 0 with the same metallicity), we find better agreement between the MEx and BPT diagnostics. Finally, we find that metallicity calibrations based on [N ii]/Hα are more biased by shocks and AGNs at high-z than the [O iii]/Hβ/[N ii]/Hα calibration.
Detection and classification of breast cancer in whole slide histopathology images using deep convolutional networks

DETECTION AND CLASSIFICATION OF BREAST CANCER IN WHOLE SLIDE HISTOPATHOLOGY IMAGES USING DEEP CONVOLUTIONAL NETWORKS Barış Geçer M.S. in Computer Engineering Advisor: Selim Aksoy July 2016 The most frequent non-skin cancer type is breast cancer which is also named one of the most deadliest diseases where early and accurate diagnosis is critical for recovery. Recent medical image processing researches have demonstrated promising results that may contribute to the analysis of biopsy images by enhancing the understanding or by revealing possible unhealthy tissues during diagnosis. However, these studies focused on well-annotated and -cropped patches, whereas a fully automated computer-aided diagnosis (CAD) system requires whole slide histopathology image (WSI) processing which is, in fact, enormous in size and, therefore, difficult to process with a reasonable computational power and time. Moreover, those whole slide biopsies consist of healthy, benign and cancerous tissues at various stages and thus, simultaneous detection and classification of diagnostically relevant regions are challenging. We propose a complete CAD system for efficient localization and classification of regions of interest (ROI) in WSI by employing state-of-the-art deep learning techniques. The system is developed to resemble organized workflow of expert pathologists by means of progressive zooming into details, and it consists of two separate sequential steps: (1) detection of ROIs in WSI, (2) classification of the detected ROIs into five diagnostic classes. The novel saliency detection approach intends to mimic efficient search patterns of experts at multiple resolutions by training four separate deep networks with the samples extracted from the tracking records of pathologists’ viewing of WSIs. The detected relevant regions are fed to the classification step that includes a deeper network that produces probability maps for classes, followed by a post-processing step for final diagnosis. iii
The Glauber dynamics for edge‐colorings of trees

Let T be a tree on n vertices and with maximum degree Δ . We show that for k≥Δ+1 the Glauber dynamics for k‐edge‐ colorings of T mixes in polynomial time in n. The bound on the number of colors is best possible as the chain is not even ergodic for k≤Δ . Our proof uses a recursive decomposition of the tree into subtrees; we bound the relaxation time of the original tree in terms of the relaxation time of its subtrees using block dynamics and chain comparison techniques. Of independent interest, we also introduce a monotonicity result for Glauber dynamics that simplifies our proof.
Ultrasonic mixing chamber as an effective tool for the biofabrication of fully graded scaffolds for interface tissue engineering

One of the main challenges of the interface-tissue engineering is the regeneration of diseased or damaged interfacial native tissues that are heterogeneous both in composition and in structure. In order to achieve this objective, innovative fabrication techniques have to be investigated. This work describes the design, fabrication, and validation of a novel mixing system to be integrated into a double-extruder bioprinter, based on an ultrasonic probe included into a mixing chamber. To validate the quality and the influence of mixing time, different nanohydroxyapatite–gelatin samples were printed. Mechanical characterization, micro-computed tomography, and thermogravimetric analysis were carried out. Samples obtained from three-dimensional bioprinting using the mixing chamber were compared to samples obtained by deposition of the same final solution obtained by manually operated ultrasound probe, showing no statistical differences. Results obtained from samples characterization allow to consider the proposed mixing system as a promising tool for the fabrication of graduated structures which are increasingly being used in interface-tissue engineering.
Loss of autophagy in chondrocytes causes severe growth retardation

ABSTRACT Chondrogenesis is accompanied by not only cellular renovation, but also metabolic stress. Therefore, macroautophagy/autophagy is postulated to be involved in this process. Previous reports have shown that suppression of autophagy during chondrogenesis causes mild growth retardation. However, the role of autophagy in chondrocyte differentiation still largely remains unclear. Here, we show the important role of autophagy on chondrogenesis. The transition of mesenchymal cells to chondrocytes was severely impaired by ablation of Atg7, a gene essential for autophagy. Mice lacking Atg7 after the transition exhibited phenotypes severer than mutant mice in which Atg7 was removed before the transition. Atg7-deficient chondrocytes accumulated large numbers of glycogen granules, hardly proliferate and died specifically in the proliferative zone without any ER-stress signal. Our results suggest that the suppression of autophagy in prechondrogenic cells drives compensatory mechanism(s) that mitigate defective chondrogenesis, and that autophagy participates in glycogenolysis to supply glucose in avascular growth plates. Abbreviations DDIT3/CHOP: DNA damage inducible transcript 3; ER: endoplasmic reticulum; NFE2L2/NRF2: nuclear factor, erythroid derived 2, like 2; SQSTM1/p62: sequestosome 1; STBD1: starch-binding domain-containing protein 1
Long-term outcomes following kidney transplantation from donors with acute kidney injury.

BACKGROUND Kidneys from deceased donors with acute kidney injury (AKI) are more likely to be discarded because of concerns for poor outcomes after transplantation. The aim of this study was to determine the long-term outcomes of a large cohort of patients transplanted utilizing kidneys from deceased donors with acute kidney injury. METHODS All patients receiving a deceased donor kidney transplant during a recent 10-year period were included. Acute Kidney Injury Network (AKIN) criteria were used to classify the donors. Donor kidneys with more than 10% cortical necrosis or more than mild chronic changes were discarded. The primary outcome is the combined endpoint of death or graft loss. RESULTS The cohort included 1,313 kidneys from 974 donors, AKIN stage 0 (no AKI) in 319 (24.3%), stage 1 in 370 (28.2%), stage 2 in 177 (13.5) and stage 3 in 447 (34.0%). Estimated 5-year graft survival (95% CI) was 78.5% (72.5-84.5), 77.8% (72.8-82.1), 83.8% (76.8-88.9) and 84.6% (79.5-88.7) for AKIN donor stage 0 to 3, respectively (log-rank p=0.10). After adjusting for baseline differences, the HR (95% CI) for the combined endpoint for the AKIN stage 3 group (relative to AKIN 0 group) was 0.70 (0.45-1.10). DGF occurred in 44.6% and 75.4% of AKIN 2 and 3 groups, as compared to 33.9% and 33.5% in AKIN 0 and 1 (p<.001). CONCLUSION We conclude that transplanting selected kidneys from deceased donors with AKI with preimplantation biopsy showing less than 10% cortical necrosis and no more than mild chronic changes have excellent long-term graft survival.
Impact of a standard versus collective-efficacy enhanced intervention to increase physical activity among mothers

Abstract Objective: Mothers have lower moderate-to-vigorous physical activity than non-mothers and this negatively impacts health. Group dynamics interventions have been successful for increasing physical activity, yet studies using these strategies among mothers are limited and rely on self-reported physical activity. The goal of this study was to examine the effectiveness of a collective-efficacy enhanced physical activity intervention that used group dynamics principles compared to a standard group-based intervention. Design: Mothers (N = 86) were randomly assigned to a 6-week intervention (collective-efficacy enhanced) or standard health education/walking group. Main outcome measures: participants wore pedometers for 1-week and completed a self-efficacy questionnaire at pre-intervention, post-intervention, and 3-month follow-up. Results: There were statistically significant increases in activity minutes (p = 0.05) and step counts (p = 0.049) and no changes in self-efficacy (p = 0.74) from pre- to post-intervention. There were no group by time interactions for changes in physical activity or self-efficacy. None of the changes in physical activity were maintained at follow-up. Conclusions: There is a continued need to understand how to use social factors to promote sustained physical activity among mothers.
piio 8 ^ ' 2 W 3 & The production of exopolysaccharides by Lactobacillus delbrueckii subsp . bulgaricus

Lactobacillus delbrueckii subsp. bulgaricus NCFB 2772 produced an extracellular polysaccharide when grown in a chemically defined medium with glucose or lactose as the substrate carbohydrate. The isolated extracellular polysaccharide had a sugar composition of glucose, galactose and rhamnose in a ratio of 1 : 6.8 : 0.7. The production of extracellular polysaccharides increased at higher temperatures, but the bacterium rapidly lost its polysaccharide producing ability at 47°C. Production of polysaccharides was growth-related: no polysaccharide production was found after growth had ceased. An excess carbohydrate did not result in increased polysaccharide production.
Use of Mentholated Cigarettes and Likelihood of Smoking Cessation in the United States: A Meta-Analysis.

INTRODUCTION Previous qualitative reviews have summarized evidence of an association between menthol cigarette use and likelihood of smoking cessation. The objective of this meta-analysis was to provide a quantitative summary of effect sizes, their variability, and factors related to the variability in effect size for the association between menthol use and likelihood of smoking cessation. METHODS We systematically searched Medline, PsycINFO, and Embase for prospective and cross-sectional studies of the association between menthol use and smoking cessation. We analyzed data with random effects meta-analyses and meta-regression. RESULTS Our review identified 22 reports from 19 studies of the association between menthol use and cessation. All identified study samples included only US smokers, with one exception that included both Canadian and US smokers. Our overall model did not demonstrate a significant association between menthol use and cessation; however, menthol users were significantly less likely to quit among blacks/African American smokers (odds ratio = 0.88). CONCLUSIONS Among blacks/African Americans predominantly in the US menthol users have approximately 12% lower odds of smoking cessation compared to non-menthol users. This difference is likely the result of the tobacco industry's ongoing marketing influence on the black/African American Community, suggesting that a menthol ban may have a unique public health benefit for black/African American smokers by encouraging quitting behavior. IMPLICATIONS This study adds a quantitative summary of the association between menthol cigarette use and smoking cessation in the United States. Findings of an association with lower likelihood of cessation among black/African American smokers, likely resulting from the tobacco industry's marketing influence, support the ban of menthol flavoring as part of a comprehensive tobacco control effort to increase cessation among black/African American smokers.