Miracle-dz/UniFAR-FTUs huggingface dataset:
CUTE: constrained and unconstrained testing environment

The purpose of this article is to discuss the scope and functionality of a versatile environment for testing small- and large-scale nonlinear optimization algorithms. Although many of these facilities were originally produced by the authors in conjunction with the software package LANCELOT, we believe that they will be useful in their own right and should be available to researchers for their development of optimization software. The tools can be obtained by anonymous ftp from a number of sources and may, in many cases, be installed automatically. The scope of a major collection of test problems written in the standard input format (SIF) used by the LANCELOT software package is described. Recognizing that most software was not written with the SIF in mind, we provide tools to assist in building an interface between this input format and other optimization packages. These tools provide a link between the SIF and a number of existing packages, including MINOS and OSL. Additionally, as each problem includes a specific classification that is designed to be useful in identifying particular classes of problems, facilities are provided to build and manage a database of this information. There is a Unix and C shell bias to many of the descriptions in the article, since, for the sake of simplicity, we do not illustrate everything in its fullest generality. We trust that the majority of potential users are sufficiently familiar with Unix that these examples will not lead to undue confusion.
Apoptosis in human sperm: its correlation with semen quality and the presence of leukocytes.

BACKGROUND Apoptosis plays an important role in regulating spermatogenesis. However, the biological significance of apoptosis in ejaculated sperm is not yet clear. This study set out to investigate how apoptosis correlates with semen quality and the presence of seminal leukocytes. METHODS Fifty-seven semen samples from the male partners of infertile couples were classified as normal or abnormal according to World Health Organization guidelines. Flow cytometry was used to evaluate sperm populations and seminal leukocytes. Preliminary flow cytometry analysis using 6-carboxyfluoresceindiacetate (6-CFDA), which identifies live cells, and propidium iodide (PI), which stains only dead cells, was performed in order to pinpoint the sperm region accurately. Having thus gated the sperm population, bivariate Annexin V/PI analysis was then carried out in order to measure the percentage of apoptotic and necrotic sperm and the apoptotic index (the ratio between apoptotic:live sperm). Leukocytes were counted by the standard peroxidase test and by flow cytometry using monoclonal antibody (mAb) anti-CD45 or anti-CD53. RESULTS No significant differences in the apoptotic index and the percentage of live and apoptotic sperm were detected between the subjects with normal and abnormal semen. A significant inverse correlation between sperm concentration and the apoptotic index was observed only in the normal sperm group. There was no correlation between the concentration of leukocytes, detected either by peroxidase or by mAb anti-CD45 or anti-CD53, either with the percentage of apoptotic sperm or with the apoptotic index. In contrast, the ratio between CD45 positive leukocytes and sperm showed a significant correlation with the apoptotic index. A weaker correlation was found when leukocytes were counted by peroxidase, while no correlation was observed using mAb anti-CD53. CONCLUSIONS Sperm apoptosis did not seem to be correlated with semen quality. In the absence of genito-urinary infection, one of the main functions of seminal leukocytes is probably to provide for the removal of apoptotic sperm.
Functional‐Mixed Effects Models for Candidate Genetic Mapping in Imaging Genetic Studies

The aim of this paper is to develop a functional‐mixed effects modeling (FMEM) framework for the joint analysis of high‐dimensional imaging data in a large number of locations (called voxels) of a three‐dimensional volume with a set of genetic markers and clinical covariates. Our FMEM is extremely useful for efficiently carrying out the candidate gene approaches in imaging genetic studies. FMEM consists of two novel components including a mixed effects model for modeling nonlinear genetic effects on imaging phenotypes by introducing the genetic random effects at each voxel and a jumping surface model for modeling the variance components of the genetic random effects and fixed effects as piecewise smooth functions of the voxels. Moreover, FMEM naturally accommodates the correlation structure of the genetic markers at each voxel, while the jumping surface model explicitly incorporates the intrinsically spatial smoothness of the imaging data. We propose a novel two‐stage adaptive smoothing procedure to spatially estimate the piecewise smooth functions, particularly the irregular functional genetic variance components, while preserving their edges among different piecewise‐smooth regions. We develop weighted likelihood ratio tests and derive their exact approximations to test the effect of the genetic markers across voxels. Simulation studies show that FMEM significantly outperforms voxel‐wise approaches in terms of higher sensitivity and specificity to identify regions of interest for carrying out candidate genetic mapping in imaging genetic studies. Finally, FMEM is used to identify brain regions affected by three candidate genes including CR1, CD2AP, and PICALM, thereby hoping to shed light on the pathological interactions between these candidate genes and brain structure and function.
Technology and Information Sharing in Disaster Relief

This paper seeks to examine the extent to which technological advances can enhance inter-organizational information sharing in disaster relief. Our case is the Virtual OSOCC (On-Site Operations Coordination Centre) which is a part of the Global Disaster Alert and Coordination System (GDACS) under the United Nations Office for Coordination of Humanitarian Affairs (UN OCHA). The online platform, which has been developing for more than a decade, provides a unique insight into coordination behaviour among disaster management agencies and individual actors. We build our study on the analysis of a complete database of user interaction including more than 20,000 users and 11,000 comments spread across approximately 300 disaster events. Controlling for types and severities of the events, location-specific vulnerabilities, and the overall trends, we find that the introduction of new features have led to increases in user activity. We supplement the data-driven approach with evidence from semi-structured interviews with administrators and key users, as well as a survey among all users specifically designed to capture and assess the elements highlighted by both interviews and data analysis.
An Empirical Two-sided Equilibrium Search Model of the Real Estate Market

Two-sided search is an important feature of the Real Estate market (REM). Existing empirical equilibrium search models assume that only one side of the market searches and, thus, can not adequately describe this market. We specify a two-sided equilibrium search model of the REM that incorporates five very important characteristics of the REM: a) buyers' and sellers' search behavior, b) heterogeneity in agents' motivation to trade, c) transaction costs, d) a trading mechanism with posting prices and bargaining, and e) the availability of an online advertising technology. The model is estimated using Maximum Likelihood methods and Multiple Listing Services data. We use the estimated model to analyze how information displayed in real estate ads on the internet affect prices and agent’s search behavior. Our estimates suggest that, on average, only 3% of the relevant information tha t home-buyers collect before making a purchase decision is obtained through online ads. Furthermore, we find that improvements in online information displayed by Real Estate ads decrease equilibrium prices but increase the time that a property stays on the market.
Fine structure in the red algae III. A general survey of cell-wall structure in the red algae

A general survey of cell-wall structure in the red algae has been carried out using the methods of X -ray diffraction analysis and electron microscopy. The fifteen species all show a similar wall structure consisting of numerous lamellae each of which is made up of random micro-fibrils embedded in an amorphous matrix. The X -ray diagrams obtained from several species are complicated by the existence of crystalline floridean starch, but nevertheless reveal the absence of cellulose I.
The Adherence Estimator: a brief, proximal screener for patient propensity to adhere to prescription medications for chronic disease

ABSTRACT Objective: To conceptualize, develop, and provide preliminary psychometric evidence for the Adherence Estimator – a brief, three-item proximal screener for the likelihood of non-adherence to prescription medications (medication non-fulfillment and non-persistence) for chronic disease. Research design and methods: Qualitative focus groups with 140 healthcare consumers and two internet-based surveys of adults with chronic disease, comprising a total of 1772 respondents, who were self-reported medication adherers, non-persisters, and non-fulfillers. Psychometric tests were performed on over 150 items assessing 14 patient beliefs and skills hypothesized to be related to medication non-adherence along a proximal–distal con-tinuum. Psychometric tests included, but were not limited to, known-groups discriminant validity at the scale and item level. The psychometric analyses sought to identify: (1) the specific multi-item scales that best differentiated self-reported adherers from self-reported non-adherers (non-fulfillers and non-persisters) and, (2) the single best item within each prioritized multi-item scale that best differentiated self-reported adherers from self-reported non-adherers (non-fulfillers and non-persisters). Results: The two rounds of psychometric testing identified and cross-validated three proximal drivers of self-reported adherence: perceived concerns about medications, perceived need for medications, and perceived affordability of medications. One item from each domain was selected to include in the Adherence Estimator using a synthesis of psychometric results gleaned from classical and modern psychometric test theory. By simple summation of the weights assigned to the category responses of the three items, a total score is obtained that is immediately interpretable and completely transparent. Patients can be placed into one of three segments based on the total score – low, medium, and high risk for non-adherence. Sensitivity was 88% – of the non-adherers, 88% would be accurately classified as medium or high risk by the Adherence Estimator. The three risk groups differed on theoretically-relevant variables external to the Adherence Estimator in ways consistent with the hypothesized proximal-distal continuum of adherence drivers. Conclusions: The three-item Adherence Estimator measures three proximal beliefs related to intentional non-adherence (medication non-fulfillment and non-persistence). Preliminary evidence of the validity of the Adherence Evidence supports its intended use to segment patients on their propensity to adhere to a newly-prescribed prescription medication. The Adherence Estimator is readily scored and is easily interpretable. Due to its brevity and transparency, it should prove to be practical for use in everyday clinical practice and in disease management for adherence quality improvement. Study limitations related to sample representation and self reports of chronic disease and adherence behaviors were discussed.
Bandwidth Enhancement of SIW Horn Antenna Loaded With Air-Via Perforated Dielectric Slab

A substrate integrated waveguide (SIW) horn antenna loaded with air-via perforated dielectric slab for bandwidth enhancement is proposed in this letter. The narrow impedance bandwidth of the planar horn antenna is mainly resulting from the discontinuity between the substrate and air. By simply drilling air-vias with different diameters in the substrate extended from the horn aperture, a smooth transition from substrate to air can be achieved, which can enhance the impedance bandwidth of the antenna in much degree. Measured results show that the enhanced impedance bandwidth of 40% from 16 to 24 GHz is obtained with the return loss |S11| below -10 dB. In addition, stable radiation patterns are observed over the entire operating band.
Personal pronouns with determining functions in Australian languages

This paper analyses the adnominal use of personal pronouns in a sample of 75 Australian languages. We develop two arguments. First, we argue that in all of the adnominal uses examined, the personal pronoun has a determiner-like function, showing both the functional properties and some of the behaviour of more typical determiner categories like demonstratives or articles. We support this analysis with evidence from positioning tendencies, semantics and discourse functions, and indications of grammaticization in some languages. Secondly, we show that this phenomenon is relatively widespread in Australia, occurring in about half of the languages examined here. We identify five potential geographic clusters, one or two of which can be analyzed as areally determined groupings around a centre with incipient grammaticization. From a typological perspective, these data present new evidence for a somewhat under-studied pathway to nominal determination, in addition to better-studied pathways involving demonstratives, numerals or adjectives.
Measurement of endogenous plasma thrombopoietin in patients with acquired aplastic anaemia by a sensitive enzyme‐linked immunosorbent assay

We measured the endogenous plasma concentration of thrombopoietin (TPO) in 76 patients with acquired aplastic anaemia (AA) by a sensitive sandwich enzyme‐linked immunosorbent assay (ELISA). The plasma TPO concentrations were significantly higher in AA patients when compared to healthy control subjects (P < 0.0001) and there was a significant negative correlation between plasma TPO concentrations and platelet counts in 54 AA patients who had not received any platelet transfusions prior to sampling. On the other hand, there was no statistically significant correlation between the TPO concentrations and platelet counts in 22 AA patients who had previously received platelet transfusions.
Autoimmunity as a trigger for structural bone damage in rheumatoid arthritis

Abstract Bone loss is a central feature of rheumatoid arthritis (RA). It is considered to represent a sign of irreversible structural damage triggered by chronic inflammation. Recent evidence, however, suggests that autoantibodies are an important and earlier driver for bone damage in RA. This article summarizes current evidence for the role of RA-related autoantibodies in mediating bone loss. Rheumatoid factor and antibodies recognizing modified (citrullinated) proteins are the central features of autoimmunity in RA patients. Despite being used as diagnostic markers for many years, ascertaining the differentiation of RA from other forms of inflammatory arthritides, the role of these antibodies as pathogenic players has long been unrecognized. Recently, several pieces of evidence suggested that bone-resorbing osteoclasts are highly responsive to RA-related autoantibodies, providing a novel link between autoimmunity and bone. These developments have allowed unraveling the underlying mechanisms, which are responsible for the well-known clinical observation that RA-related autoantibodies are associated with a more severe disease course. At present, rheumatoid factor and antibodies recognizing citrullinated proteins are considered as potent osteoclast inducers and triggers for bone loss in arthritis.
Senecavirus A: An Emerging Vesicular Infection in Brazilian Pig Herds.

Vesicular diseases are clinically and economically important infections that affect farm animals. North American studies have suggested that Senecavirus A infection might be associated with a vesicular disease in pigs known as porcine idiopathic vesicular disease (PIVD). In the beginning of 2015, outbreaks of porcine vesicular disease have occurred in six Brazilian states from three geographical regions. Official diagnostic tests were performed with negative results for classical vesicular diseases of compulsory reporting. This study investigated Senecavirus A infection in PIVD outbreaks in which other aetiological agents were ruled out. A primer set was designed to amplify a 542-bp product size of VP3/VP1 region of Senecavirus A genome in RT-PCR assay. Primer specificity was analysed in silico and in porcine biological specimens. For this, clinical specimens were collected from eight pig herds affected with PIVD, including vesicular fluid (n = 4) and swabs (n = 7) and scrapings of ruptured vesicles and ulcerative lesions (n = 5) from weaned and adult pigs. Clinically healthy animals (n = 52) of PIVD-affected and non-affected pig herds also were evaluated for Senecavirus A infection. The 16 samples from PIVD-affected animals were positive for Senecavirus A in the RT-PCR assay, while none of the clinically healthy pigs were detected with the virus. Sequencing analysis revealed high nucleotide (87.6-98.5%) and amino acid (95-99.4%) similarities to SVV-01 prototype and other Senecavirus A strains from North American pigs. Primer set presented herein was suitable for molecular characterization of Senecavirus A. The results suggest that Senecavirus A was the aetiological agent of the vesicular disease outbreaks in the evaluated pig herds. This is the first study to report the Senecavirus A infection in clinically affected pigs outside of North America. Senecavirus A was considered a novel emerging pathogen associated with an important vesicular disease in Brazil.
Moving towards disease modification in inflammatory bowel disease therapy

Purpose of review The inflammatory bowel diseases (IBDs) are chronic disabling conditions. Despite the benefits of anti-tumor necrosis factor (TNF)-&agr; agents in improving quality of life and reducing the need for surgeries, overall only one-third of patients are in clinical remission at 1 year and loss of response is frequent. It seems clear that treatment must go beyond alleviation of symptoms in IBD. It is important that treatment targets in IBD will ensure mucosal healing and deep remission. Recent findings The induction of deep remission might be the best way to alter the natural course of these diseases by preventing disability and bowel damage. New disability indices and the new Crohn's disease damage score have recently been developed and they can be used to evaluate the long-term effect on patients and as new endpoints in trials. Early intervention with disease-modifying anti-IBD drugs (DMAIDs) should be considered in patients with poor prognostic factors. Summary New therapeutic targets in IBD patients who failed anti-TNF-&agr; therapy are urgently required, and tofacitinib, vedolizumab and ustekinumab appear to be the most promising drugs. Herein, we review the new and current trends in IBD therapy, with the final aim of changing disease course and patients’ lives by both improving quality of life and avoiding disability.
Heat-Related Death and Mental Illness During the 1999 Cincinnati Heat Wave

During a 1999 heat wave in Cincinnati, Ohio, the Hamilton County Coroner reported 18 heat-related deaths. The Centers for Disease Control and Prevention and the Cincinnati Department of Health conducted a case–control study using surrogate case information and first-person control information to identify risk factors for mortality during the heat wave. Surrogate data were supplemented by systematic death scene investigation reports and comprehensive toxicologic screens, important sources of data that are routinely collected by the Hamilton County Coroner’s Office. The study included 17 case subjects and 34 controls from the decedents’ neighborhood. Among 17 case subjects, 8 (47.1%) had mental illness (odds ratio [OR], 14.0; 95% confidence interval [CI], 1.8–633). There was a suggestion of an interaction between age and mental health. A working air-conditioner was the strongest protective factor (OR, 0.03; 95% CI, 0–0.2). Toxicologic screening indicated that case subjects with reported mental illness and a prescription for psychotropic drugs may not have been medication compliant. Three decedents lived in group homes for people with mental illness, indicating that opportunities for prevention may have been missed. Systematic death investigations, including toxicologic screening, provide valuable information about the circumstances of heat-related death, particularly the role of medication compliance as a risk factor. Prevention programs during heat waves should target people with mental illness, especially those who take psychotropic medication.
Does malnutrition affect survival in cirrhosis? PINC (Policentrica Italiana Nutrizione Cirrosi).

A total of 1,053 cirrhotic patients were included in a prospective study to determine whether malnutrition is a risk factor for mortality in cirrhotic patients. Child-Pugh classification as well as clinical and biochemical variables were used to assess the severity of cirrhosis. Nutritional status was evaluated both by anthropometric and clinical measurements. Patients were defined as malnourished when midarm muscle area (MAMA) and/or midarm fat area (MAFA) were below the 5th percentile of an age- and sex-matched population. During follow-up, 419 patients died. The estimated survival rate was 82.7% at 1 year, 65.1% at 3 years, and 50.7% at 5 years. The presence of muscle depletion and/or of a steep reduction in fat deposits was associated with a higher risk of mortality (midarm muscle area, < 5th percentile, relative risk = 1.79; midarm fat area, < 5th percentile, relative risk = 1.35). When patients were stratified according to the Child-Pugh classification, cumulative survival was lower in patients with a reduction in muscle mass in Child-Pugh classes A and B (log rank: P = .027; P = .022, respectively) but not in class C. Conversely, a significant reduction in adipose tissue deposits appeared to have no independent impact on survival in any Child-Pugh class. When examined using a multivariate Cox proportional hazard analysis, age, sex, bilirubin, cholinesterase, ascites, and esophageal varices were selected, whereas the parameters of nutritional status were not. This suggests that malnutrition, while strongly associated with the deterioration of liver function, cannot be considered an independent risk factor for mortality in a general population of cirrhotic patients.