Miracle-dz/UniFAR-FTUs huggingface dataset:
A Minor (<50%) Signet-Ring Cell Component Associated with Poor Prognosis in Colorectal Cancer Patients: A 26-Year Retrospective Study in China

Background We performed a retrospective study to determine the cancer-specific survival of colorectal cancer patients with a component of signet-ring cells or mucin comprising < 50% of the tumor mass. Methods A total of 2454 patients seen in our hospital from 1985 to 2011 were retrospectively studied. The patients were divided into five groups according to type of cancer: signet-ring cell carcinoma (with > 50% signet-ring cell, n = 36), partial signet-ring cell carcinoma (with < 50% signet-ring cell, n = 28), mucinous adenocarcinoma (with > 50% mucin lacking signet-ring cell, n = 267), partial mucinous adenocarcinoma (with < 50% mucin lacking signet-ring cell, n = 145), and classic adenocarcinoma (with absence of either mucin or signet-ring cell, n = 1978). Results Patients with > 50% or < 50% signet-ring cell had the lowest 5-year survival rates (35.5% and 29.7%, respectively), followed by patients with > 50% mucin (48.8%). Patients who had partial mucinous adenocarcinoma with < 50% mucin and classic adenocarcinoma patients had the highest 5-year survival rates (64.8% and 65.3%, respectively). Stratified and multivariate analysis showed that signet-ring cell carcinoma, partial signet-ring cell carcinoma and mucinous adenocarcinoma were independent predictors of decreased survival (hazard ratio 1.699, P = 0.016; hazard ratio 2.182, P = 0.005; hazard ratio 1.532, P < 0.001; respectively), and partial mucinous adenocarcinoma was not (hazard ratio 1.137, P = 0.431). Conclusions Patients with a component of signet-ring cells, regardless of the extent, had poor prognoses. Patients with mucinous adenocarcinoma containing >50% mucin had poor prognoses as well, whereas those with < 50% mucin had survival rates similar to those of classic adenocarcinoma patients. Therefore, in clinical practice, patients with a component of signet-ring cells, regardless of the extent, should be given significant clinical attention.
Differential Pathway Coupling of the Activated Insulin Receptor Drives Signaling Selectivity by XMetA, an Allosteric Partial Agonist Antibody

The monoclonal antibody XMetA is an allosteric partial agonist of the insulin receptor (IR), which activates the metabolic Akt kinase signaling pathway while having little or no effect on the mitogenic extracellular signal‐regulated kinase (ERK) signaling pathway. To investigate the nature of this selective signaling, we have conducted a detailed investigation of XMetA to evaluate specific phosphorylation and activation of IR, Akt, and ERK in Chinese hamster ovary cell lines expressing either the short or long isoform of the human IR. Insulin activated both pathways, but the phosphorylation of Akt was more sensitive to the hormone than the phosphorylation of ERK. Maximally effective concentrations of XMetA elicited phosphorylation patterns similar to 40–100 pM insulin, which were sufficient for robust Akt phosphorylation, but had little effect on ERK phosphorylation. These data indicate that the preferential signaling of XMetA is due to an innate difference in pathway sensitivity of Akt versus ERK responses to IR activation and partial agonism by XMetA, rather than a separate pathway-biased mechanism. The metabolic selectivity of partial IR agonists like XMetA, if recapitulated in vivo, may be a desirable feature of therapeutic agents designed to regulate blood glucose levels while minimizing undesirable outcomes of excessive IR mitogenic activation.
Predictors of loss to follow-up among children in the first and second years of antiretroviral treatment in Johannesburg, South Africa

Background : Ninety percent of the world's 2.1 million HIV-infected children live in sub-Saharan Africa, and 2.5% of South African children live with HIV. As HIV care and treatment programmes are scaled-up, a rise in loss to follow-up (LTFU) has been observed. Objective : The aim of the study was to determine the rate of LTFU in children receiving antiretroviral treatment (ART) and to identify baseline characteristics associated with LTFU in the first year of treatment. We also explored the effect of patient characteristics at 12 months treatment on LTFU in the second year. Methods : The study is an analysis of prospectively collected routine data of HIV-infected children at the Harriet Shezi Children's Clinic (HSCC) in Soweto, Johannesburg. Cox proportional hazards models were fitted to investigate associations between baseline characteristics and 12-month characteristics with LTFU in the first and second year on ART, respectively. Results : The cumulative probability of LTFU at 12 months was 7.3% (95% CI 7.1–8.8). In the first 12 months on ART, independent predictors of LTFU were age <1 year at initiation, recent year of ART start, mother as a primary caregiver, and being underweight (WAZ ≤ −2). Among children still on treatment at 1 year from ART initiation, characteristics that predicted LTFU within the second year were recent year of ART start, mother as a primary caregiver, being underweight (WAZ ≤ −2), and low CD4 cell percentage. Conclusions : There are similarities between the known predictors of death and the predictors of LTFU in the first and second years of ART. Knowing the vital status of children is important to determine LTFU. Although HIV-positive children cared for by their mothers appear to be at greater risk of becoming LTFU, further research is needed to explore the challenges faced by mothers and other caregivers and their impact on long-term HIV care. There is also a need to investigate the effects of differential access to ART between mothers and children and its impact on ART outcomes in children.
Instrumental Evaluation of Pediatric Dysphagia: FEES Versus Videofluoroscopy

Introduction Problems with swallowing, dysphagia, can occur in infants and children, which may have devastating effects. When a child with dysphagia is not treated properly, it may cause aspiration pneumonia, gastroesophageal reflux, and inability to develop and maintain adequate nutrition and hydration, and failure to thrive. This is why it is critical to properly evaluate children that are showing signs and/or are at risk for dysphagia (Prasse & Kikano, 2009). Instrumental assessments provide images of the oral, pharyngeal, and upper esophageal phases of swallowing and are generally used to address particular diagnostic questions which may determine what type of therapy would be beneficial (Arvedson, 2008; Rogers and Arvedson, 2005). The two most common types of instrumental assessments to evaluate dysphagia are videofluoroscopy (aka Modified Barium Swallow examination, MBS, or VFSS) and FEES (aka videoendoscopy or flexible fiberoptic examination of swallowing). Over the years, there has been a debate about whether FEES/FEEST or videofluoroscopy is, or should be, the " gold-standard " for assessing dysphagia. However, there has been a lack of research that directly compares them, and an even smaller number of investigations that have concentrated on the pediatric population. The focus of this research paper is to compare and contrast the use of FEES versus MBS for pediatric dysphagia evaluations. First, a description of each instrumental evaluation tool is provided followed by a discussion of the strengths and limitations of each procedure. VFSS and FEES can be compared based on each procedure's ability to enable feedback during intervention, assess sensory threshold, evaluate and diagnose GER, provide patient comfort, and assess a wide range of appropriate candidates. There 2 are limited studies that have attempted to compare VFSS and FEES directly in their ability to assess pediatric dysphagia, but a discussion of these studies can provide some insight for clinicians contemplating the use of instrumental assessment procedures. Instrumental Assessments FEES/FEES-ST Flexible endoscopic examination of swallowing (FEES) is one type of instrumental evaluation that is generally performed by a SLP and a pediatric otolaryngologist both working together. A flexible endoscope is inserted through the client's nose and is held in place so that the examiner(s) can observe the events that transpire right before and after the pharyngeal swallow. During this evaluation, the examiner(s) may also wish to administer a sensory test (FEESST), which uses air pressure to test laryngeal reflexes (Arvedson, 2008). VFSS Another instrumental examination is the videofluoroscopic swallow study …
Effects of Chronic Treatment With l-Arginine on Atherosclerosis in ApoE Knockout and ApoE/Inducible NO Synthase Double-Knockout Mice

Objective—l-Arginine serves as a substrate for the formation of NO by the NO synthase (NOS) enzymes. In some studies, dietary supplementation of l-arginine reduces atherosclerosis through the restoration of NO release and improvement in endothelial function. In the present study, we investigate the effect of l-arginine supplementation on the development of atherosclerosis in a mouse model. Methods and Results—Apolipoprotein E (apoE) knockout (ko) and apoE/inducible NOS (iNOS) double-ko mice were fed a western-type diet with or without l-arginine supplementation in the drinking water (25 g/L). l-Arginine did not affect the lesion area after 16 weeks or 24 weeks in apoE ko mice. However, l-arginine negates the protective effect of iNOS gene deficiency. In contrast to apoE/iNOS dko mice without arginine supplementation, lesion areas were increased in apoE/iNOS double-ko mice with arginine supplementation at 24 weeks. This was associated with an increase in thiobarbituric acid-reactive malondialdehyde adducts, nitrotyrosine staining within lesions, and a decrease in the ratio of reduced tetrahydrobiopterin to total biopterins. Conclusions—Although l-arginine supplementation does not affect lesion formation in the western-type diet-fed apoE ko mice, it negates the protective effect of iNOS gene deficiency in this model. This raises the possibility that l-arginine supplementation may paradoxically contribute to, rather than reduce, lesion formation by mechanisms that involve lipid oxidation, peroxynitrite formation, and NOS uncoupling.
English Corpus Linguistics

Corpus linguistics is a research method which draws on authentic language examples, collected and organized into 'corpora', or searchable 'bodies' of data. The method was established in the 1960s, and has rapidly developed since then. Now in its second edition, this book provides a step-by-step guide on how to create and analyze linguistic corpora. It has been extensively updated to reflect the most recent developments in this ever-evolving field, and now covers the empirical foundation of corpus-based research, new methodological considerations that guide the creation of a corpus, new kinds of research that can be conducted on corpora, and the most up-to-date information on how qualitative and quantitative analyses of corpora are conducted. Theoretical approaches are introduced in an accessible, easy-to-read way, and the book is illustrated with a wide range of different linguistic corpora, making it essential reading for researchers and students in a number of subfields of linguistics.
Borchers' Commutation Relations and Modular Symmetries

Recently Borchers has shown that in a theory of local observables, certain unitary and antiunitary operators, which are obtained from an elementary construction suggested by Bisognano and Wichmann, commute with the translation operators like Lorentz boosts and \pct-operators, respectively. We conclude from this that as soon as the operators considered implement {\em any} symmetry, this symmetry can be fixed up to at most some translation. As a symmetry, we admit any unitary or antiunitary operator under whose adjoint action any algebra of local observables is mapped onto an algebra which can be localized somewhere in Minkowski space.
Helicobacter pylori infection.

INTRODUCTION The principal effect of Helicobacter pylori infection is lifelong chronic gastritis, affecting up to 20% of younger adults but 50% to 80% of adults born in resource-rich countries before 1950. METHODS AND OUTCOMES We conducted a systematic review and aimed to answer the following clinical questions: What are the effects of H pylori eradication treatment in people with a confirmed duodenal ulcer, a confirmed gastric ulcer, confirmed gastro-oesophageal reflux disease (GORD), confirmed non-ulcer dyspepsia, uninvestigated dyspepsia, localised B cell lymphoma of the stomach, and non-steroidal anti-inflammatory drug (NSAID)-related peptic ulcers? What are the effects of H pylori eradication treatment for preventing NSAID-related peptic ulcers in people with or without previous ulcers or dyspepsia? What are the effects of H pylori eradication treatment on the risk of developing gastric cancer? Do H pylori eradication treatments differ in their effects? We searched: Medline, Embase, The Cochrane Library, and other important databases up to September 2007 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA). RESULTS We found 58 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions. CONCLUSIONS In this systematic review we present information relating to the effectiveness and safety of the following interventions: effects of H pylori eradication in different populations; relative effects of triple regimens, quadruple regimens, and sequential regimens.
Short Form (SF‐36) Health Survey Measures Are Associated With Decreased Adherence Among Urban African Americans With Severe, Poorly Controlled Hypertension

The objective of this study was to determine whether an association exists between Short Form (SF‐36) Health Survey measures and nonadherence among urban African Americans with poorly controlled hypertension. A total of 158 African Americans were admitted to an urban academic hospital for severe, uncontrolled hypertension. The main outcome measure was self‐reported nonadherence to antihypertensive medications using a validated instrument. For every 10‐point increase in Physical Component Summary (PCS) score, an individual was almost two times more likely to report being nonadherent (odds ratio, 1.94; 95% confidence interval, 1.30–2.90; P<.01). A significant interaction (P=.05) was observed between the physical functioning and mental health subscales. Individuals with high physical functioning and low mental health scores displayed the lowest adherence rate. These results suggest that high physical functioning, especially if associated with poor mental health, increases the likelihood of nonadherence to antihypertensive regimens among urban African Americans. The SF‐36 may serve as an effective clinical tool that identifies patients at risk for nonadherence and, more importantly, may improve clinicians’ understanding of nonadherence, allowing for discussions about antihypertensive medications to be tailored to individual patients. J Clin Hypertens (Greenwich). 2011;13:385–390. ©2010 Wiley Periodicals, Inc.
Quantized conductive filament formed by limited Cu source in sub-5nm era

For the first time, we have investigated the resistive switching characteristics in extreme size (sub-5nm) device. Less than 5nm effective electrode radius is confirmed by conductive-AFM and FIB-TEM analysis. The conductive filament source (Cu ions) is limited by applying novel fabrication technology. Due to the limited Cu source, we observe the quantized formation of conductive path, which results in the distinguishable conductance states and shows the feasibility of multi-bit operation. By controlling the motion of Cu ions precisely, ideal selection behavior for xpoint memory application was achieved.
Statistical and Computational Methods for Comparative Proteomic Profiling Using Liquid Chromatography-Tandem Mass Spectrometry

The combined method of LC-MS/MS is increasingly being used to explore differences in the proteomic composition of complex biological systems. The reliability and utility of such comparative protein expression profiling studies is critically dependent on an accurate and rigorous assessment of quantitative changes in the relative abundance of the myriad of proteins typically present in a biological sample such as blood or tissue. In this review, we provide an overview of key statistical and computational issues relevant to bottom-up shotgun global proteomic analysis, with an emphasis on methods that can be applied to improve the dependability of biological inferences drawn from large proteomic datasets. Focusing on a start-to-finish approach, we address the following topics: 1) low-level data processing steps, such as formation of a data matrix, filtering, and baseline subtraction to minimize noise, 2) mid-level processing steps, such as data normalization, alignment in time, peak detection, peak quantification, peak matching, and error models, to facilitate profile comparisons; and, 3) high-level processing steps such as sample classification and biomarker discovery, and related topics such as significance testing, multiple testing, and choice of feature space. We report on approaches that have recently been developed for these steps, discussing their merits and limitations, and propose areas deserving of further research.
Thyroid Cytology: The Japanese System and Experience at Yamashita Thyroid Hospital

In Japan, fine-needle aspiration (FNA) cytology is the most important diagnostic modality for triaging patients with thyroid nodules. A clinician (endocrinologist, endocrine surgeon, or head and neck surgeon) generally performs FNA cytology at the outpatient clinic, and ultrasound (US)-guided FNA is widespread because US is extremely common and most clinicians are familiar with it. Although almost all FNA thyroid samples are examined by certified cytopathologists and pathologists, some clinicians assess cytological specimens themselves. In Japan, there are two clinical guidelines regarding the management of thyroid nodules. One is the General Rules for the Description of Thyroid Cancer (GRDTC) published by the Japanese Society of Thyroid Surgery (JSTS) in 2005, and the other is the national reporting system for thyroid FNA cytology published by the Japan Thyroid Association in 2013 (Japanese system). Although the Bethesda System for Reporting Thyroid Cytopathology (Bethesda system) is rarely used in Japan, both the GRDTC and Japanese system tried to incorporate the Bethesda system so that the cytological diagnoses would be compatible with each other. The essential point of the Japanese system is stratification of follicular neoplasm (FN) into three subgroups based on cytological features in order to reduce unnecessary diagnostic thyroidectomy, and this system has been successful in stratifying the risk of malignancy in FN patients at several high-volume thyroid surgery centers. In Japan, the measurement of thyroglobulin and/or calcitonin in FNA needle washings is often used as an adjunct for diagnosis of possible cervical lymph node metastasis when FNA cytology is performed.
Fingerprint Classification Using Orientation Field Flow Curves

Manual fingerprint classification proceeds by carefully inspecting the geometric characteristics of major ridge curves in a fingerprint image. We propose an automatic approach of identifying the geometric characteristics of ridges based on curves generated by the orientation field called orientation field flow curves (OFFCs). The geometric characteristics of OFFCs are analyzed by studying the isometric maps of tangent planes as a point traverses along the curve from one end to the other. The path traced by the isometric map consists of several important features such as sign change points and locations as well as values of local extremas, that uniquely identify the inherent geometric characteristics of each OFFC. Moreover, these features are invariant under changes of location, rotation and scaling of the fingerprint. We have applied our procedure on the NIST4 database consisting of 4,000 fingerprint images without any training. Classification into four major fingerprint classes (arch, left-loop, right-loop and whorl) with no reject options yields an accuracy of 94.4. %
Now casting of traffic state by GPS data. The metropolitan area of Rome

In the near future a large amount of data on individual vehicle position and speed for the full road network will be available from GPS systems. This possibility opens new research perspectives for prevention and governance of congestion and of traffic criticalities. A prototype model, developed under Pegasus Project sponsored by the Italian Ministry of Industry, is working in Rome. The system is based on the real time reconstruction of the speed, density and flux on the whole metropolitan road network using a low sampling rate GPS data set. We present the state of the art of the project discussing its strength and weakness. We then show the results of the data analysis for the month of May 2010.
THE KINETICS AND THERMODYNAMICS OF REVERSIBLE DENATURATION OF CRYSTALLINE SOYBEAN TRYPSIN INHIBITOR

Crystalline soybean trypsin inhibitor protein undergoes denaturation on heating which is reversed on cooling. In the range of temperature of 35 to 50°C. a solution of the protein consists of a mixture of native and denatured forms in equilibrium with each other. The equilibrium is only slowly established and its final value at any temperature is the same whether a heated, denatured solution of the protein is cooled to the given temperature or whether a fresh solution is raised to that temperature. The kinetics of reversible denaturation of the soybean protein as well as the reversal of denaturation is that of a reversible unimolecular reaction, each process consisting at a given temperature of the same two simultaneous reactions acting in opposite directions. The experimental data on the effect of temperature on the velocity and the equilibrium constants of the opposing reaction were utilized in evaluating the reaction energies and activation energies. The reaction energies for denaturation were found to be as follows:— Change in total heat of reaction ΔH = 57,000 calories per mole Change in entropy of reaction ΔS = 180 calories per degree per mole The heat of activation ΔH 1 ‡ for denaturation = 55,000 The heat of activation ΔH 2 ‡ for the reversal of denaturation = –1900 The entropy ΔS 1 ‡ for denaturation = 95 The entropy ΔS 2 ‡ for reversal of denaturation = –84
Benchmarking GPUs to tune dense linear algebra

We present performance results for dense linear algebra using recent NVIDIA GPUs. Our matrix-matrix multiply routine (GEMM) runs up to 60% faster than the vendor's implementation and approaches the peak of hardware capabilities. Our LU, QR and Cholesky factorizations achieve up to 80-90% of the peak GEMM rate. Our parallel LU running on two GPUs achieves up to ~540 Gflop/s. These results are accomplished by challenging the accepted view of the GPU architecture and programming guidelines. We argue that modern GPUs should be viewed as multithreaded multicore vector units. We exploit blocking similarly to vector computers and heterogeneity of the system by computing both on GPU and CPU. This study includes detailed benchmarking of the GPU memory system that reveals sizes and latencies of caches and TLB. We present a couple of algorithmic optimizations aimed at increasing parallelism and regularity in the problem that provide us with slightly higher performance.
Reflections on the Approach to Treatment of a Mycologic Disaster

On 18 September 2012, health authorities began to react to a multistate outbreak of fungal meningitis of unprecedented magnitude, traceable to 3 lots of preservative-free methylprednisolone compounded in one pharmacy ([1][1]). The steroids had been used mostly for epidural injection, largely causing