Miracle-dz/UniFAR-FTUs huggingface dataset:
ABO chimerism with a minor allele detected by the peptide nucleic acid-mediated polymerase chain reaction clamping method.

Discrepancy of results of ABO groups between red cell testing and serum testing is a significant issue in transfusion medicine1. One of its reported causes is blood chimerism, which shows mixed-field agglutination. However, mixed-field agglutination can be seen in various situations, including ABO-incompatible stem cell transplantation, recent transfusions of type-O red blood cells in a non-O recipient, and rare ABO subgroups such as B3 and chimera. Several molecular approaches have been employed to identify chimerism, namely ABO genotyping, human leucocyte antigen typing and DNA short tandem repeat assays2. These methods can typically detect three or more alleles of a chimera. However, some chimeras with a minor allele population might be overlooked because of preferential amplification of the major allele during ordinary polymerase chain reaction (PCR) analysis. We report a case of blood chimerism in which B red cells accounted for less than 1% of the whole population. The B allele in peripheral blood mononuclear cells could not be identified by direct sequencing of ordinary PCR product involving exons 6 and 7 of the ABO gene, but was revealed using peptide nucleic acid (PNA)-mediated PCR clamping.
Safe Parallel Programming in an Interpreted Language

Parallel programming is increasingly important with the advent of multicore processors. However, modern software is difficult to parallelize because of the high degree of modularization. It is unclear whether a piece of code is parallel if it calls other functions. Dynamic languages such as Ruby, Python, and Matlab represent modularization to the extreme. A program, also known as a script, requires interpretation for every statement, calling a whole host of functions from parsing to execution. Because of the complexity of the interpreter and the dynamic nature of script code, scripting languages are among the most difficult to parallelize. In this paper, safe parallelization means to parallelize a sequential program with the guarantee that the parallelized version produces the same result as the original sequential code. In other words, safety means sequential equivalence. There are generally three ways to ensure safety. Consider a sequential loop as the target program to parallelize. The first way is static. A compiler analyzes the loop and determines whether it is parallel. Static parallelization means that the loop is parallel in all executions. The second way is dynamic. Immediately before executing the loop, a run-time library determines whether the loop is parallel. The third way is speculative. The loop is run in parallel speculatively. If conflicts are detected in the parallel execution, the conflicting part is rolled back and re-run sequentially. This paper uses the third way and describes a system that speculatively parallelizes a Ruby script to ensure safety. In the past, most speculation systems were for automatic parallelization and were not user programmable [2, 5, 10]. Then a number of interfaces appeared, including safe future in Java [13], ordered transactions using TLS hardware [12], and possibly parallel region (PPR) in the BOP (behaviorbased parallelization) system [4, 6, 14], and multi-threaded transactions [9]. These are effectively hints of parallelism. Dependence hints were introduced in the BOP system as a way to suggest possible dependences between operations in different PPRs [7]. In this paper, we adapt the BOP interfaces for use in Ruby. 2. Safe Parallel Ruby
Osteoporosis and osteoarthritis: shared mechanisms and epidemiology

Purpose of reviewOsteoporosis and osteoarthritis are different diseases, with differences in risk factors, bone mineral density (BMD), BMI, phenotype, morbidity and mortality. We review new data on the role of bone metabolism in osteoporosis and osteoarthritis. Recent findingsThe insights in the common convergent and divergent risk factors between osteoarthritis and osteoporosis have resulted in new findings on the role of BMD, BMI, falls, genetics and epigenetics in the pathophysiology of both diseases and on the increased fracture risk in osteoporosis and osteoarthritis. The relation between BMD, BMI and fracture risk in osteoarthritis is dependent on the stage, definition and location of the osteoarthritis and method of BMD measurement. It has been suggested that osteoarthritis should be further specified in terms of bone involvement. SummaryThese new findings open the way to better understand the bone subtypes of osteoarthritis (osteoporotic, bone forming and erosive) and the common and different ways bone is involved in osteoporosis and osteoarthritis. Much can be expected from further prospective studies, when taking into account the heterogeneous nature of both osteoporosis and osteoarthritis.
Onset of gravitational collapse of colloidal gels: an optical microscopy study

Colloidal gels are ubiquitous in daily life, such as paint. A colloidal gel can support its own weight for a finite delay time in gravity. This delay time sets the shelf life of many products. Hence, understanding the gravitational stability of colloidal gels could promote their industrial application. This work presents results on the mesoscopic scale (∼ 10 μm) aiming to bridge macroscopic observations with the microscopic perspective in previous studies. In a model system of colloids + polymers, typical kinds of gel collapse were studied using fluorescence microscopy. Two collapse mechanisms are found for low and high colloidal volume fractions (φc), respectively. At low φc, denser debris falls through and breaks the gel structure. At high φc, solvent droplets rise to the top of a gel allowing the solvent to be expelled from the gel quickly. For gels with intermediate φc, these two mechanisms cooperate. Large-scale hydrodynamic remixing and recirculation are observed before the onset of gel collapse, emphasizing that hydrodynamics is crucial. The imaging results also suggest that the menisci of the samples play an important role of the gel collapse. By eliminating most of the curved meniscus, the collapse of gel can be postponed. Previous hypothesis for gel collapse is based on the competition between the yield stress of gel and gravitational stress. Our results on large and small particle gels show similar collapse behaviours both on macroand meso-scopic scales. Considering that the yield stress varies sensitively with the size of the particle, this similarity suggests different mechanisms should be developed for the collapse of small and large particle gels.
Ametista: a mini-toolkit for exploring new window management techniques

Although the HCI research community has contributed a number of metaphors, interaction techniques and layout algorithms to improve window management tasks, most of these ended as prototypes and only a few were implemented in real window managers. In this paper, we present Ametista, a mini-toolkit designed to facilitate the exploration of new window management techniques using both low-fidelity prototyping and a high-fidelity approach based on X Window application redirection.
How Does Contributors' Involvement Influence the Build Status of an Open-Source Software Project?

The recent introduction of the pull-based development model promoted agile development practices such as Code Reviews and Continuous Integration (CI). CI, in particular, is currently a standard development practice in open-source software (OSS) projects. Although it is well-known that OSS contributors have different involvements (e.g., while some developers drive the project, there is a long tail of peripheral developers), little is known about how the contributor's degree of participation can influence the build status of an OSS project. Through TravisTorrent's dataset, we compare the success rates of builds made by casual and non-casual contributors and what factors on their contributions may influence the build result. Our results suggest that there is no representative difference between their build success (they are similar in 85% of the analyzed projects), meaning that being a casual contributor is not a strong indicator for creating failing builds. Also, factors like the size of their contributions and the number of project configurations (jobs) have the potential of impacting the build success.
Open Access Research Article the Prevalence of Norovirus in Returning International Travelers with Diarrhea

Background: There is a high incidence of diarrhea in traveling populations. Norovirus (NV) infection is a common cause of diarrhea and is associated with 7% of all diarrhea related deaths in the US. However, data on the overall prevalence of NV infection in traveling populations is limited. Furthermore, the prevalence of NV amongst travelers returning to Europe has not been reported. This study determined the prevalence of NV among international travelers returning to Germany from over 50 destinations in and outside Europe. Methods: Stool samples of a total of 104 patients with a recent (< 14days) history of international travel (55 male, mean age 37 yrs.) were tested for the presence of NV genogroup (GG) I and II infection using a sensitive and well established quantitative RT PCR method. 57 patients experienced diarrhea at the time of presentation at the Department of Infectious Diseases & Tropical Medicine. The remaining 47 patients had no experience of diarrhea or other gastrointestinal symptoms for at least 14 days prior to their date of presentation at our institute. Results: In our cohort, NV infection was detected in 15.7% of returning travelers with diarrhea. The closer to the date of return symptoms appeared, the higher the incidence of NV, ranging as high as 21.2% within the first four days after return. Conclusions: In our cohort, NV infection was shown to be frequent among returning travelers especially in those with diarrhea, with over 1/5 of diarrhea patients tested positive for NV within the first four days after their return to Germany. Due to this prevalence, routine testing for NV infection and hygienic precautions may be warranted in this group. This is especially applicable to patients at an increased risk of spreading the disease, such as healthcare workers, teachers or food-handlers. Background An increased incidence of diarrhea can be detected in traveling populations [1]. In industrialized countries noroviruses (NV) are presently recognized as the most common cause of diarrhea in the adult population, both for epidemic [2] and sporadic [3] cases of diarrhea. It is estimated that they cause up to 85% of all viral enteritis worldwide [4]. Despite the high rate of recovery generally associated with NV infection, up to 7% of all diarrhea-related deaths in the US are thought to be caused by NV [5]. Thus, NV enteritis can be expected to cause signifi
Nest: A Nested-Predicate Scheme for Fault Tolerance

Introduces a nested-predicate scheme for fault tolerance, called Nest. Nest provides a formal comprehensive model for fault-tolerant parallel algorithms and a general methodology for designing reliable applications for multiprocessor systems. The model relies on the formalization of concepts for fault tolerance by means of three nested system predicates and on properties ruling their interrelationships. This rigorous framework facilitates the study of the specific properties that enable an algorithm to tolerate faults. The consequence of that is the outline of systematic design techniques that can be used to add fault tolerance properties to algorithms while preserving their functional characteristics. >
SIRT1 Deacetylates and Inhibits SREBP-1C Activity in Regulation of Hepatic Lipid Metabolism*

The SIRT1 deacetylase inhibits fat synthesis and stimulates fat oxidation in response to fasting, but the underlying mechanisms remain unclear. Here we report that SREBP-1c, a key lipogenic activator, is an in vivo target of SIRT1. SIRT1 interaction with SREBP-1c was increased during fasting and decreased upon feeding, and consistently, SREBP-1c acetylation levels were decreased during fasting in mouse liver. Acetylated SREBP-1c levels were also increased in HepG2 cells treated with insulin and glucose to mimic feeding conditions, and down-regulation of p300 by siRNA decreased the acetylation. Depletion of hepatic SIRT1 by adenoviral siRNA increased acetylation of SREBP-1c with increased lipogenic gene expression. Tandem mass spectrometry and mutagenesis studies revealed that SREBP-1c is acetylated by p300 at Lys-289 and Lys-309. Mechanistic studies using acetylation-defective mutants showed that SIRT1 deacetylates and inhibits SREBP-1c transactivation by decreasing its stability and its occupancy at the lipogenic genes. Remarkably, SREBP-1c acetylation levels were elevated in diet-induced obese mice, and hepatic overexpression of SIRT1 or treatment with resveratrol, a SIRT1 activator, daily for 1 week decreased acetylated SREBP-1c levels with beneficial functional outcomes. These results demonstrate an intriguing connection between elevated SREBP-1c acetylation and increased lipogenic gene expression, suggesting that abnormally elevated SREBP-1c acetylation increases SREBP-1c lipogenic activity in obese mice. Reducing acetylation of SREBP-1c by targeting SIRT1 may be useful for treating metabolic disorders, including fatty liver, obesity, and type II diabetes.
Optical molecular imaging detects changes in extracellular pH with the development of head and neck cancer

Noninvasive localized measurement of extracellular pH in cancer tissues can have a significant impact on the management of cancer. Despite its significance, there are limited approaches for rapid and noninvasive measurement of local pH in a clinical environment. In this study, we demonstrate the potential of noninvasive topical delivery of Alexa‐647 labeled pHLIP (pH responsive peptide conjugated with Alexa Fluor® 647) to image changes in extracellular pH associated with head and neck squamous cell carcinoma using widefield and high resolution imaging. We report a series of preclinical analyses to evaluate the optical contrast achieved after topical delivery of Alexa‐647 labeled pHLIP in intact fresh human tissue specimens using widefield and high‐resolution fluorescence imaging. Using topical delivery, Alexa‐647 labeled pHLIP can be rapidly delivered throughout the epithelium of intact tissues with a depth exceeding 700 µm. Following labeling with Alexa‐647 labeled pHLIP, the mean fluorescent contrast increased four to eight fold higher in clinically abnormal tissues as compared to paired clinically normal biopsies. Furthermore, the imaging approach showed significant differences in fluorescence contrast between the cancer and the normal biopsies across diverse patients and different anatomical sites (unpaired comparison). The fluorescence contrast differences between clinically abnormal and normal tissues were in agreement with the pathologic evaluation. Topical application of fluorescently labeled pHLIP can detect and differentiate normal from cancerous tissues using both widefield and high resolution imaging. This technology will provide an effective tool to assess tumor margins during surgery and improve detection and prognosis of head and neck cancer.
Mechanical properties of polymer grafted nanoparticle composites

Abstract Polymer nanocomposites have improved mechanical, optical and thermal properties compared to traditional thermoplastics. To study the impact of grafted brush–matrix interactions on the mechanical properties of nanoparticle filled polymers, uniaxial tensile testing with digital image correlation (DIC) was done on polystyrene (PS) grafted SiO2 in low molecular weight (MW) (N ∼ P), N = degree of polymerization of grafted brush, P = degree of polymerization of matrix, and high MW (2N = P) matrices at different loadings. The low matrix MW composites had higher strength than high MW composites at high loading but lower strength than the pure matrix. The high matrix MW composites had higher toughness at low loadings. SEM images of fracture surfaces revealed particle debonding and plastic void growth in the high toughness samples. The results show that the P/N ratio of polymer grafted nanoparticle composites is important for controlling the mechanical properties of polymer nanocomposites. Graphical Abstract
Integrated bioprocess to boost cellulosic bioethanol titers and yields

Among potential alternative liquid fuels, bioethanol is the widest utilized transportation fuels and mainly made from grains. Cellulosic biofuels provide environmental benefits not available from grain or sugar-based biofuels and are considered as a solid foundation to meet transportation fuels needs in a low-carbon economy, albeit with electrified vehicles and other technical advances. The objective of this research was to develop and optimize various bioprocessing units to boost cellulosic bioethanol titers and yields in order to accelerate the commercialization of cellulosic bioethanol production. The results showed high-solids biomass bioconversion (12%, w/v) was inefficient in the laboratory rotary shaker. However, a horizontal reactor with good mixing was effective for high solids loading (20%, w/v), yielding 75 g/L of glucose. To achieve the minimal economical ethanol distillation requirement of 40 g/L, integrated bioprocesses were conducted to boost ethanol titers and yields through co-fermentation of starchy grain and cellulosic biomass. The maximum ethanol concentration (68.7 g/L) was achieved at the corn flour and hydrothermaltreated corn stover ratio of 12:12 using raw starch granular enzyme with the ethanol yield of 86.0%. Co-fermentation of starchy substrate with hydrolysate liquor from saccharified biomass was able to significantly enhance ethanol concentration and reduce energy cost for distillation without sacrificing ethanol yields. These results indicated integration of first and second generation ethanol production could significantly accelerate the commercialization of cellulosic biofuel production. Novel technology, modified simultaneous saccharification and fermentation, was firstly established to enhance ethanol titers and yields, which achieved high ethanol titers of 72.3 g/L at high biomass loadings of 30% (w/v) with 70.0% ethanol yield. Integrated bioprocess to boost cellulosic bioethanol titers and yields
Is Hyperglycemia a Cardiovascular Risk Factor?

Patients with diabetes show an increased vascular morbidity and mortality that reduces their life expectancy by ~5–15 years (depending on the age at diagnosis) (1). There is convincing evidence from epidemiological and pathophysiological studies that hyperglycemia per se is largely responsible for the harmful effects of the disease. As recently shown by clinical trials, treatment of this condition may reduce cardiovascular events and mortality, and several therapies should be considered: initiating early and individualized treatment and avoiding hypoglycemia. As shown in the Multiple Risk Factor Intervention Trial, at any given level of major cardiovascular risk factors, diabetes is associated with an odds ratio of 2–4 for cardiovascular mortality compared with nondiabetic subjects (2). These results were confirmed by the European Prospective Investigation of Cancer and Nutrition (EPIC Norfolk) study (3) and a recent analysis of the Atherosclerosis Risk in Communities (ARIC) study (4). Furthermore, a recently published 18-year follow-up study from Finland demonstrated a similar impact of type 1 and type 2 diabetes on cardiovascular mortality. The adjusted hazard ratios compared with age-matched subjects without diabetes were 5.2 and 4.9 for type 1 and type 2 diabetes, respectively (5). Thus, today evidence exists on long-term follow-up population-based studies in patients with type 1 and type 2 diabetes. This evidence clearly suggests that hyperglycemia is a key risk factor not only for diabetes-related disease, but also for cardiovascular and all-cause mortality. On the basis of these long-term observations, one can assume an increment of cardiovascular disease per increase of 1 unit (%) A1C of ~18% (6). As shown in numerous prospective studies, the deleterious effects of dysglycemia (fasting and postprandial hyperglycemia) develop before diabetes is diagnosed. In the Glucose Tolerance in Acute Myocardial Infarction study of patients with acute coronary syndrome, abnormal glucose tolerance was the strongest independent …
Automatic Background Knowledge Selection for Matching Biomedical Ontologies

Ontology matching is a growing field of research that is of critical importance for the semantic web initiative. The use of background knowledge for ontology matching is often a key factor for success, particularly in complex and lexically rich domains such as the life sciences. However, in most ontology matching systems, the background knowledge sources are either predefined by the system or have to be provided by the user. In this paper, we present a novel methodology for automatically selecting background knowledge sources for any given ontologies to match. This methodology measures the usefulness of each background knowledge source by assessing the fraction of classes mapped through it over those mapped directly, which we call the mapping gain. We implemented this methodology in the AgreementMakerLight ontology matching framework, and evaluate it using the benchmark biomedical ontology matching tasks from the Ontology Alignment Evaluation Initiative (OAEI) 2013. In each matching problem, our methodology consistently identified the sources of background knowledge that led to the highest improvements over the baseline alignment (i.e., without background knowledge). Furthermore, our proposed mapping gain parameter is strongly correlated with the F-measure of the produced alignments, thus making it a good estimator for ontology matching techniques based on background knowledge.
Stylometric model for detecting oath expressions: A case study for Quranic texts

The Quranic oath is God’s emphasizing the importance or truthfulness of a concept. Oaths are multifaceted, rich expressions, in which a single oath contains a line of meaning and a variety of aspects. This study proposes a new stylometric model for detecting apparent and narrative oaths. Toward this end, two types of application-specific features from a stylometric perspective—structural and content-specific features—were examined. The stylometric features were extracted, and a Bayesian network was constructed to model such features. The stylometric model of oaths was then evaluated through a series of machine-learning experiments using various classifiers: the Bayesian network, a decision tree, instance-based learning, and a neural network. These classification experiments focused on applying stylometric features in apparent and narrative oaths. The experiments covered two datasets: the entire Quran and the smaller dataset of Juz ’ ‘ Amma . The results led to two main conclusions. First, stylometric application-specific features are best used in their entirety—both structural-based and content-specific—rather than as two separate entities. Second, applying stylometric features was more significant in Juz ’ ‘ Amma , in which 40% of its surahs (chapters) contain oath statements. Finally, the stylometric model was extended for oath styles detection using three additional stylometric features—syntactic, character, and lexical, and it was analyzed using statistical approach.