Miracle-dz/UniFAR-FTUs huggingface dataset:
Does this patient with liver disease have cirrhosis?

CONTEXT Among adult patients with liver disease, the ability to identify those most likely to have cirrhosis noninvasively is challenging. OBJECTIVE To identify simple clinical indicators that can exclude or detect cirrhosis in adults with known or suspected liver disease. DATA SOURCES We searched MEDLINE and EMBASE (1966 to December 2011) and reference lists from retrieved articles, previous reviews, and physical examination textbooks. STUDY SELECTION We retained 86 studies of adequate quality that evaluated the accuracy of clinical findings for identifying histologically proven cirrhosis. DATA EXTRACTION Two authors independently abstracted data (sensitivity, specificity, and likelihood ratios [LRs]) and assessed methodological quality. Random-effects meta-analyses were used to calculate summary LRs across studies. RESULTS Among the 86 studies, 19,533 patients were included in this meta-analysis, among whom 4725 had biopsy-proven cirrhosis (prevalence rate, 24%; 95% CI, 20%-28%). Many physical examination and simple laboratory tests increase the likelihood of cirrhosis, though the presence of ascites (LR, 7.2; 95% CI, 2.9-12), a platelet count <160 x 10(3)/μL (LR, 6.3; 95% CI, 4.3-8.3), spider nevi (LR, 4.3; 95% CI 2.4-6.2), or a combination of simple laboratory tests with the Bonacini cirrhosis discriminant score >7 (LR, 9.4; 95% CI, 2.6-37) are the most frequently studied, reliable, and informative results. For lowering the likelihood of cirrhosis, the most useful findings are a Lok index <0.2 (a score created from the platelet count, serum aspartate aminotransferase and alanine aminotransferase, and prothrombin international normalized ratio; LR, 0.09; 95% CI, 0.03-0.31); a platelet count ≥160 x 10(3)/μL (LR, 0.29; 95% CI, 0.20-0.39); or the absence of hepatomegaly (LR, 0.37; 95% CI, 0.24-0.51). The overall impression of the clinician was not as informative as the individual findings or laboratory combinations. CONCLUSIONS For identifying cirrhosis, the presence of a variety of clinical findings or abnormalities in a combination of simple laboratory tests that reflect the underlying pathophysiology increase its likelihood. To exclude cirrhosis, combinations of normal laboratory findings are most useful.
Controlled motion strain measurement using lateral speckle tracking in Achilles tendons during healing

Ultrasound elastography imaging is being increasingly used to indicate the functional properties of musculoskeletal pathologies. Usually, this involves a real-time free-hand acquisition which has questionable consistency and does not provide a material deformation that is representative of the material function. This paper presents a novel method for acquiring quantitative ultrasound lateral strain images of in-vivo Achilles tendons in a controlled manner using a computer controlled foot articulation device and a novel 2D multiscale, multi-compression, sub-pixel precision block matching algorithm. The method has been applied to a longitudinal study of 21 patients with Achilles tendon rupture which have repeated data points taken over 24 weeks of therapy. The controlled lateral motion results are compared to the more conventional freehand axial-decompression method, and also against clinical measures. The results show that the controlled lateral motion strain images have a smaller standard deviation of average value than the freehand decompression motion (σlat = 0.77%, σcomp =1.74%) and a tighter fitting to a strain improvement model which followed the same form as clinical measures of patient healing over the group (Rlat2 = 0.78, Rcomp2 = 0.34).
Random points in halfspheres

A random spherical polytope Pn in a spherically convex set K⊂Sd as considered here is the spherical convex hull of n independent, uniformly distributed random points in K. The behaviour of Pn for a spherically convex set K contained in an open halfsphere is quite similar to that of a similarly generated random convex polytope in a Euclidean space, but the case when K is a halfsphere is different. This is what we investigate here, establishing the asymptotic behaviour, as n tends to infinity, of the expectation of several characteristics of Pn, such as facet and vertex number, volume and surface area. For the Hausdorff distance from the halfsphere, we obtain also some almost sure asymptotic estimates. © 2016 Wiley Periodicals, Inc. Random Struct. Alg. , 50, 3–22, 2017
Query enrichment for web-query classification

Web-search queries are typically short and ambiguous. To classify these queries into certain target categories is a difficult but important problem. In this article, we present a new technique called query enrichment, which takes a short query and maps it to intermediate objects. Based on the collected intermediate objects, the query is then mapped to target categories. To build the necessary mapping functions, we use an ensemble of search engines to produce an enrichment of the queries. Our technique was applied to the ACM Knowledge Discovery and Data Mining competition (ACM KDDCUP) in 2005, where we won the championship on all three evaluation metrics (precision, F1 measure, which combines precision and recall, and creativity, which is judged by the organizers) among a total of 33 teams worldwide. In this article, we show that, despite the difficulty of an abundance of ambiguous queries and lack of training data, our query-enrichment technique can solve the problem satisfactorily through a two-phase classification framework. We present a detailed description of our algorithm and experimental evaluation. Our best result for F1 and precision is 42.4% and 44.4%, respectively, which is 9.6% and 24.3% higher than those from the runner-ups, respectively.
Tracking performance across software revisions

Repository-based revision control systems such as CVS, RCS, Subversion, and GIT, are extremely useful tools that enable software developers to concurrently modify source code, manage conflicting changes, and commit updates as new revisions. Such systems facilitate collaboration with and concurrent contribution to shared source code by large developer bases. In this work, we investigate a framework for "performance-aware" repository and revision control for Java programs. Our system automatically tracks behavioral differences across revisions to provide developers with feedback as to how their change impacts performance of the application. It does so as part of the repository commit process by profiling the performance of the program or component, and performing automatic analyses that identify differences in the dynamic behavior or performance between two code revisions. In this paper, we present our system that is based upon and extends prior work on calling context tree (CCT) profiling and performance differencing. Our framework couples the use of precise CCT information annotated with performance metrics and call-site information, with a simple tree comparison technique and novel heuristics that together target the cause of performance differences between code revisions without knowledge of program semantics. We evaluate the efficacy of the framework using a number of open source Java applications and present a case study in which we use the framework to distinguish two revisions of the popular FindBugs application.
Challenge of Reducing Perinatal Mortality in Rural Congo: Findings of a Prospective, Population-based Study

Each year, an estimated six million perinatal deaths occur worldwide, and 98% of these deaths occur in lowand middle-income countries. These estimates are based on surveys in both urban and rural areas, and they may underrepresent the problem in rural areas. This study was conducted to quantify perinatal mortality, to identify the associated risk factors, and to determine the most common causes of early neonatal death in a rural area of the Democratic Republic of the Congo (DRC). Data were collected on 1,892 births. Risk factors associated with perinatal deaths were identified using multivariate analysis with logistic regression models. Causes of early neonatal deaths were determined by physician-review of information describing death. The perinatal mortality rate was 61 per 1,000 births; the stillbirth rate was 30 per 1,000 births; and the early neonatal death rate was 32 per 1,000 livebirths. Clinically-relevant factors independently associated with perinatal death included: low birthweight [odds ratio (OR)=13.51, 95% confidence interval (CI) 7.82-23.35], breech presentation (OR)=12.41; 95% CI 4.62-33.33), lack of prenatal care (OR=2.70, 95% CI 1.81-4.02), and parity greater than 4 (OR=1.93 95% CI 1.11-3.37). Over one-half of early neonatal deaths (n=37) occurred during the first two postnatal days, and the most common causes were low birthweight/prematurity (47%), asphyxia (34%), and infection (8%). The high perinatal mortality rate in rural communities in the DRC, approximately one-half of which is attributable to early neonatal death, may be modifiable. Specifically, deaths due to breech presentation, the second most common risk factor, may be reduced by making available emergency obstetric care. Most neonatal deaths occur soon after birth, and nearly three-quarters are caused by low birthweight/prematurity or asphyxia. Neonatal mortality might be reduced by targeting interventions to improve neonatal resuscitation and care of larger preterm infants.
Relationships Among Cerebrospinal Fluid Biomarkers in Dementia of the Alzheimer Type

Cerebrospinal fluid (CSF) contains proteins known to be involved in the pathogenesis of Alzheimer disease (AD), including amyloid-related proteins, tau protein and apolipoprotein E. While the CSF concentrations of these proteins have been compared in subjects with and without dementia of the Alzheimer type (DAT), they have not been simultaneously assessed in carefully staged DAT subjects and control subjects to examine correlations among them. In this study, CSF concentrations of soluble amyloid precursor protein (sAPP), two forms of &bgr;-amyloid protein (A&bgr;total and A&bgr;1–42), tau, and apolipoprotein E were assessed in subjects with (n = 33) and without (n = 11) DAT. Direct correlations were found between CSF concentrations of sAPP and tau and A&bgr;total, and between apolipoprotein E and A&bgr;total within the DAT subjects and within the combined group of DAT and control subjects. A weak inverse correlation was also found between CSF concentrations of tau and A&bgr;1–42 within the combined group of DAT and control subjects. Moreover, increased severity of dementia was correlated with increased CSF tau concentrations and decreased sAPP and A&bgr;total concentrations. Increased CSF concentrations of tau significantly discriminated DAT and control subjects, as did the ratios of tau to A&bgr;total and tau to A&bgr;1–42.
Effects of Nonpeptide V1 Vasopressin Receptor Antagonist SR-49059 on Infarction Volume and Recovery of Function in a Focal Embolic Stroke Model

Background and Purpose— Cerebral edema develops very early after the onset of focal cerebral ischemia and may be a major factor in early disability after an acute ischemic stroke. There have been very limited studies on the usefulness of antiedemic agents as neuroprotective agents in the setting of focal cerebral ischemia. We tested the neuroprotective effects of a new potent nonpeptide vasopressin receptor V1 antagonist, SR-49059, in a focal embolic stroke model in rats. Methods— Focal ischemic injury was induced by embolizing a preformed clot into the middle cerebral artery (MCA). Infarction volume was measured at 48 hours after the MCA occlusion. Neurological deficits, ischemic brain edema, seizure activity, and mortality and hemorrhage rates were also documented. Results— Treatment with SR-49059 (2 mg/kg), initiated immediately after MCA occlusion, significantly reduced infarction volume (P <0.05) measured at 48 hours after the arterial occlusion. In animals in which the treatment was delayed for 1 hour after MCA occlusion, infarction volume was also reduced significantly (P <0.05). Infarction volume in the rats that received the drug at 3 or 6 hours after MCA occlusion was not different from that in the vehicle-treated group. Treatment with SR-49059, when started early after the arterial occlusion, also reduced neurological deficits and ischemic brain edema. Injection of drug at a higher dose (30 mg/kg) also reduced infarction volume and improved functional recovery but was not superior to the lower dose (2 mg/kg) when the drug was administrated at 1 hour after MCA occlusion. Conclusions— Our data show that the selective vasopressin receptor antagonist SR-49059 is a potent neuroprotective agent when used early after onset of arterial occlusion in an embolic focal ischemia model in rats. Further studies are needed in stroke models to better understand its neuroprotective properties when used alone or in combination with thrombolysis.
Concurrent validity and test–retest reliability of a global positioning system (GPS) and timing gates to assess sprint performance variables

Abstract There has been no previous investigation of the concurrent validity and reliability of the current 5 Hz global positioning system (GPS) to assess sprinting speed or the reliability of integrated GPS–accelerometer technology. In the present study, we wished to determine: (1) the concurrent validity and reliability of a GPS and timing gates to measure sprinting speed or distance, and (2) the reliability of proper accelerations recorded via GPS–accelerometer integration. Nineteen elite youth rugby league players performed two over-ground sprints and were simultaneously assessed using GPS and timing gates. The GPS measurements systematically underestimated both distance and timing gate speed. The GPS measurements were reliable for all variables of distance and speed (coefficient of variation [CV] = 1.62% to 2.3%), particularly peak speed (95% limits of agreement [LOA] = 0.00 ± 0.8 km · h−1; CV = 0.78%). Timing gates were more reliable (CV = 1% to 1.54%) than equivalent GPS measurements. Accelerometer measurements were least reliable (CV = 4.69% to 5.16%), particularly for the frequency of proper accelerations (95% LOA = 1.00 ± 5.43; CV = 14.12%). Timing gates and GPS were found to reliably assess speed and distance, although the validity of the GPS remains questionable. The error found in accelerometer measurements indicates the limits of this device for detecting changes in performance.
Cysteamine S-phosphate hydrolysis by pure human alkaline phosphatases and by sera from patients with lymphoproliferative disorders.

Abstract Alkaline phosphatases (EC 3.1.3.1) purified from human placenta, neutrophils, liver, kidney, and small intestinal mucosa showed a range of Km values for p-nitrophenyl phosphate from 0.017 to 0.038 mm. The Km values for cysteamine S-phosphate were more variable and ranged from 0.09 to 1.00 mm. The ratios of the rate of hydrolysis of p-nitrophenyl phosphate to the rate of hydrolysis of cysteamine S-phosphate were similar among the multiple forms of human alkaline phosphatase (1.5 to 1.9) with a mean value of 1.7. The hydrolysis of p-nitrophenyl phosphate and cysteamine S-phosphate was also measured in 36 normal sera, and a mean value of 2.1 ± 0.5 (S.D.) was obtained from the ratios of the rate of hydrolysis of p-nitrophenyl phosphate to that of cysteamine S-phosphate. Forty sera from patients with one of the following lymphoproliferative disorders: lymphoma; myeloma; infectious mononucleosis; Hodgkin9s disease; chronic or acute lymphatic leukemia; or Burkitt9s lymphoma displayed a mean ratio of 2.0 ± 0.4. The mean ratio for 13 sera from patients with one of the following proliferative disorders, acute myeloid leukemia, lung cancer, or sarcoma, was 2.2 ± 0.3. The sera from nine patients with increased serum alkaline phosphatase levels due to pregnancy or conditions other than proliferative disorders had a mean value of 1.8 ± 0.3 for the ratio of the rate of hydrolysis of p-nitrophenyl phosphate to that of cysteamine S-phosphate. Seventeen aqueous solutions of butanol extracts of either normal granulocytes or lymphocytes had a mean ratio value of 2.0 ± 0.9. Therefore, no evidence was found for a unique alkaline phosphatase which could act as a marker for lymphoproliferative disorders through its inability to hydrolyze cysteamine S-phosphate.
Neural Stem Cell Niches in Health and Diseases

Presence of neural stem cells in adult mammalian brains, including human, has been clearly demonstrated by several studies. The functional significance of adult neurogenesis is slowly emerging as new data indicate the sensitivity of this event to several “every day” external stimuli such as physical activity, learning, enriched environment, aging, stress and drugs. In addition, neurogenesis appears to be instrumental for task performance involving complex cognitive functions. Despite the growing body of evidence on the functional significance of NSC and despite the bulk of data concerning the molecular and cellular properties of NSCs and their niches, several critical questions are still open. In this work we review the literature describing i) old and new sites where NSC niche have been found in the CNS; ii) the intrinsic factors regulating the NSC potential; iii) the extrinsic factors that form the niche microenvironment. Moreover, we analyse NSC niche activation in iv) physiological and v) pathological conditions. Given the not static nature of NSCs that continuously change phenotype in response to environmental clues, a unique “identity card” for NSC identification is still lacking. Moreover, the multiple location of NSC niches that increase in diseases, leaves open the question of whether and how these structures communicate throughout long distance. We propose a model where all the NSC niches in the CNS may be connected in a functional network using the threads of the meningeal net as tracks.
Predictors of the location of multiple sclerosis relapse

Background: While clinical relapses are the defining feature of relapsing–remitting multiple sclerosis (RRMS), their characteristics vary widely from patient to patient. This study sought to identify predictors of MS relapse location. Based on the current literature, two potential predictors were identified: treatment with interferon β (IFNB) and location of previous relapse. Methods: Patients with RRMS were identified from the UCSF MS Center database who underwent at least 3 months of treatment with IFNB or glatiramer acetate (GA). The relapse immediately preceding the initiation of treatment (pretreatment relapse) and the first relapse occurring after the initiation of treatment (on-treatment relapse) were coded as affecting the spinal cord (SC), optic nerve (ON), brainstem/cerebellum (BC) or cerebrum. Logistic regression was performed to identify independent predictors of on-treatment relapse location. Results: The 134 IFNB and 56 GA patients did not differ in gender, race, age at symptom onset (30.3 years) or disease duration at the start of treatment (5.7 years). Patients with pretreatment SC relapses had increased odds of having on-treatment SC compared with non-SC relapses (OR 2.31, p = 0.013); the same tendency for localisation occurred with BC (OR 3.05, p = 0.013) and ON (OR 3.63, p = 0.011) relapses. Additionally, patients who relapsed on treatment had a higher SC (but not ON or BC) relapse risk when they were receiving IFNB compared with GA (OR 2.05, p = 0.041), independent of pretreatment relapse location. Conclusion: These results show a tendency for patients to have localised exacerbations, which could be mediated by genetic or immunological factors. In addition, and to be confirmed in subsequent studies, IFNB treatment may influence SC relapse risk.
Recent advances in amplify-and-forward two-hop relaying

In this article we review an important class of wireless cooperation protocols known as amplify-and-forward relaying. One or more low-complexity relay nodes assist the communication between sources and destinations without having to decode the signal. This makes AF relaying transparent to modulation and coding of the source/destination communication protocol. It is therefore a highly flexible technology that also qualifies for application in heterogeneous networks comprising many nodes of different complexity or even standards. Recently, two-way relaying was introduced, which is readily combined with AF relaying. It is a spectrally efficient protocol that allows for bidirectional communication between sources and destinations. In order to investigate the potential of wireless AF relaying, we introduce three distributed network scenarios that differ in the amount of cooperation between nodes. New challenges arise in those networks, and we discuss approaches to overcome them. For the most general case of a completely distributed system, we present coherent relaying solutions that offer a distributed spatial multiplexing gain even for single-antenna nodes. Based on real-world experiments, we validate the feasibility of all schemes in our laboratory.
Cytomegalovirus Activates Interferon Immediate-Early Response Gene Expression and an Interferon Regulatory Factor 3-Containing Interferon-Stimulated Response Element-Binding Complex

ABSTRACT Interferon establishes an antiviral state in numerous cell types through the induction of a set of immediate-early response genes. Activation of these genes is mediated by phosphorylation of latent transcription factors of the STAT family. We found that infection of primary foreskin fibroblasts with human cytomegalovirus (HCMV) causes selective transcriptional activation of the alpha/beta-interferon-responsive ISG54 gene. However, no activation or nuclear translocation of STAT proteins was detected. Activation of ISG54 occurs independent of protein synthesis but is prevented by protein tyrosine kinase inhibitors. Further analysis revealed that HCMV infection induced the DNA binding of a novel complex, tentatively called cytomegalovirus-induced interferon-stimulated response element binding factor (CIF). CIF is composed, at least in part, of the recently identified interferon regulatory factor 3 (IRF3), but it does not contain the STAT1 and STAT2 proteins that participate in the formation of interferon-stimulated gene factor 3. IRF3, which has previously been shown to possess no intrinsic transcriptional activation potential, interacts with the transcriptional coactivator CREB binding protein, but not with p300, to form CIF. Activating interferon-stimulated genes without the need for prior synthesis of interferons might provide the host cell with a potential shortcut in the activation of its antiviral defense.
Dropping out from school: a cross country review of literature

This paper provides an in-depth review and analysis of literature on dropping out from school, and focuses on children who have gained access, but fail to complete a basic education cycle. The main discussion is around why and how children drop out from school. Here drop out is not presented as a distinct event, but rather a process where a range of supply-demand factors interact to influence schooling access. The paper looks at literature in relation to household, community and social contexts of dropping out, as well as school supply and practices. It also explores what research is saying around pre-cursors to dropping out and factors which may influence retention. Finally, the study identifies gaps in research around dropping out and how CREATE research could address some of these.