Miracle-dz/UniFAR-FTUs huggingface dataset:
Methylmalonic aciduria cblB type: characterization of two novel mutations and mitochondrial dysfunction studies

Methylmalonic aciduria (MMA) cblB type is caused by mutations in the MMAB gene, which codes for the enzyme adenosine triphosphate (ATP): cobalamin adenosyltransferase (ATR). This study reports differences in the metabolic and disease outcomes of two pairs of siblings with MMA cblB type, respectively harbouring the novel changes p.His183Leu/p.Arg190dup (P1 and P2) and the previously described mutations p.Ile96Thr/p.Ser174fs (P3 and P4). Expression analysis showed p.His183Leu and p.Arg190dup to be destabilizing mutations. Both were associated with reduced ATR stability and a shorter half‐life than wild‐type ATR. Analysis of several parameters related to oxidative stress and mitochondrial function showed an increase in reactive oxygen species (ROS) content, a decrease in mitochondrial respiration and changes in mitochondria morphology and structure in patient‐derived fibroblasts compared to control cells. The impairment in energy production and the presence of oxidative stress and fission of the mitochondrial reticulum suggested mitochondrial dysfunction in cblB patients' fibroblasts. The recovery of mitochondrial function should be a goal in efforts to improve the clinical outcome of MMA cblB type.
Enhancement of speech intelligibility in near-end noise conditions with phase modification

Post-processing methods can be used in mobile communications to improve the intelligibility of speech in adverse near-end noise conditions. This study proposes a phase spectrum modiﬁ-cation method for intelligibility enhancement in mobile devices. The method ﬁrst modiﬁes the phase spectrum of speech in order to reduce the amplitude range of the signal. The amplitude level is then equalized to that of the unprocessed speech hence resulting in ampliﬁcation of signal energy. The performance of the proposed method was evaluated in comparison to a known post-processing method with an objective intelligibility metric in multiple noise conditions. Results indicate that the proposed post-processing method improves speech intelligibility over the reference method.
On the effectiveness of risk prediction based on users browsing behavior

Users are typically the final target of web attacks: criminals are interested in stealing their money, their personal information, or in infecting their machines with malicious code. However, while many aspects of web attacks have been carefully studied by researchers and security companies, the reasons that make certain users more "at risk" than others are still unknown. Why do certain users never encounter malicious pages while others seem to end up on them on a daily basis? To answer this question, in this paper we present a comprehensive study on the effectiveness of risk prediction based only on the web browsing behavior of users. Our analysis is based on a telemetry dataset collected by a major AntiVirus vendor, comprising millions of URLs visited by more than 100,000 users during a period of three months. For each user, we extract detailed usage statistics, and distill this information in 74 unique features that model different aspects of the user's behavior. After the features are extracted, we perform a correlation analysis to see if any of them is correlated with the probability of visiting malicious web pages. Afterwards, we leverage machine learning techniques to provide a prediction model that can be used to estimate the risk class of a given user. The results of our experiments show that it is possible to predict with a reasonable accuracy (up to 87%) the users that are more likely to be the victims of web attacks, only by analyzing their browsing history.
Parsing bidimensional de estructuras DAG mediante el algoritmo SCP y su aplicación al reconocimiento de habla

This work describes an strategy for the integration of speech recognition, unification-based parsing and dialogue management and its application to spoken dialogue systems. The strategy is based on the use of the notion of breaking points implemented by the SCP (Syntactic Constraints Propagation) parsing algorithm. This format allows the representation of word lattices and their direct manipulation by SCP.
A Real Time Hand Tracking System for Interactive Applications

In vision based hand tracking systems color plays an important role for detection. Skin color detection is widely used in different interactive applications, e.g. face and hand tracking, detecting people in video databases. This paper implements an effective hand tracking technique which is based on color detection. In this techniques based on the color distribution the segmentation of hand from background will take place in a real time. This technique provides to main benefits: The process of tracking is fast as the segmentation process is performed simultaneously in a specified area surrounding the hand. This technique is highly robust under different lightning conditions. To check the performance of the implemented technique a number of experiments have been performed. The implemented technique will be useful in various real time interactive applications, such as gesture recognition, augmented reality, virtual reality etc.
Defective Human Leukocyte Antigen Class I-associated Antigen Presentation Caused by a Novel β2-Microglobulin Loss-of-function in Melanoma Cells*

The major histocompatibility complex class I molecules consist of three subunits, the 45-kDa heavy chain, the 12-kDa β2-microglobulin (β2m), and an ∼8-9-residue antigenic peptide. Without β2m, the major histocompatibility complex class I molecules cannot assemble, thereby abolishing their transport to the cell membrane and the subsequent recognition by antigen-specific T cells. Here we report a case of defective antigen presentation caused by the expression of a β2m with a Cys-to-Trp substitution at position 25 (β2mC25W). This substitution causes misfolding and degradation of β2mC25W but does not result in complete lack of human leukocyte antigen (HLA) class I molecule expression on the surface of melanoma VMM5B cells. Despite HLA class I expression, VMM5B cells are not recognized by HLA class I-restricted, melanoma antigen-specific cytotoxic T lymphocytes even following loading with exogenous peptides or transduction with melanoma antigen-expressing viruses. Lysis of VMM5B cells is restored only following reconstitution with exogenous or endogenous wild-type β2m protein. Together, our results indicate impairment of antigenic peptide presentation because of a dysfunctional β2m and provide a mechanism for the lack of close association between HLA class I expression and susceptibility of tumor cells to cytotoxic T lymphocytes-mediated lysis in malignant diseases.
Sentence Pair Scoring: Towards Unified Framework for Text Comprehension

We review the task of Sentence Pair Scoring, popular in the literature in various forms - viewed as Answer Sentence Selection, Semantic Text Scoring, Next Utterance Ranking, Recognizing Textual Entailment, Paraphrasing or e.g. a component of Memory Networks. We argue that all such tasks are similar from the model perspective and propose new baselines by comparing the performance of common IR metrics and popular convolutional, recurrent and attention-based neural models across many Sentence Pair Scoring tasks and datasets. We discuss the problem of evaluating randomized models, propose a statistically grounded methodology, and attempt to improve comparisons by releasing new datasets that are much harder than some of the currently used well explored benchmarks. We introduce a unified open source software framework with easily pluggable models and tasks, which enables us to experiment with multi-task reusability of trained sentence model. We set a new state-of-art in performance on the Ubuntu Dialogue dataset.
COI1, a jasmonate receptor, is involved in ethylene-induced inhibition of Arabidopsis root growth in the light

Plant response to stress is orchestrated by hormone signalling pathways including those activated by jasmonates (JAs) and by ethylene, both of which stunt root growth. COI1 is a JA receptor and is required for the known responses to this hormone. It was observed that the coi1 mutant, which is largely unresponsive to growth inhibition by JAs, was also partially unresponsive to growth inhibition by ethylene and by its immediate precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), in the light but not in the dark. Although COI1 was required for this response to ACC, other components of the JA signal perception pathway were not. Mutants selected for insensitivity to ethylene, including etr1, ein2, and ein3, showed greater ACC-induced root growth inhibition in the light than in the dark. However, the double mutants etr1;coi1, ein2;coi1, and ein3;coi1, and coi1 seedlings treated with silver ions to block the ethylene receptors showed almost complete unresponsiveness to ACC-induced root growth inhibition in the light. The light requirement for the COI1-mediated growth inhibition by ACC was for long photoperiods, and the ACC response was not abolished by mutations in the known photoreceptors. The complementation assay indicated that SCF complex assembly was not required for COI1 function in the ACC response, in contrast to the JA response. It is concluded that COI1 is required for the light-dependent, JA-independent, root growth inhibition by ethylene.
Matched Gene Selection and Committee Classifier for Molecular Classification of Heterogeneous Diseases

Microarray gene expressions provide new opportunities for molecular classification of heterogeneous diseases. Although various reported classification schemes show impressive performance, most existing gene selection methods are suboptimal and are not well-matched to the unique characteristics of the multicategory classification problem. Matched design of the gene selection method and a committee classifier is needed for identifying a small set of gene markers that achieve accurate multicategory classification while being both statistically reproducible and biologically plausible. We report a simpler and yet more accurate strategy than previous works for multicategory classification of heterogeneous diseases. Our method selects the union of one-versus-everyone (OVE) phenotypic up-regulated genes (PUGs) and matches this gene selection with a one-versus-rest support vector machine (OVRSVM). Our approach provides even-handed gene resources for discriminating both neighboring and well-separated classes. Consistent with the OVRSVM structure, we evaluated the fold changes of OVE gene expressions and found that only a small number of high-ranked genes were required to achieve superior accuracy for multicategory classification. We tested the proposed PUG-OVRSVM method on six real microarray gene expression data sets (five public benchmarks and one in-house data set) and two simulation data sets, observing significantly improved performance with lower error rates, fewer marker genes, and higher performance sustainability, as compared to several widely-adopted gene selection and classification methods. The MATLAB toolbox, experiment data and supplement files are available at http://www.cbil. ece.vt. edu/software.htm.
Effect of combination therapy of angiotensin-converting enzyme inhibitor plus calcium channel blocker on urinary albumin excretion in hypertensive microalbuminuric patients with type II diabetes.

It has been demonstrated that antihypertensive treatment of hypertensive diabetic patients is quite effective in preventing macrovascular and microvascular complications and improving prognosis. Nevertheless, the target blood pressure level of antihypertensive treatment in hypertensive diabetic patients with microalbuminuria (i.e., with early diabetic nephropathy) remains to be established. In this study, we evaluated the effect of intensive blood pressure control (diastolic blood pressure <80 mmHg) on urinary albumin excretion in hypertensive, type II diabetic patients with microalbuminuria. We examined the effects of a combination therapy using an angiotensin-converting enzyme (ACE) inhibitor plus a long-acting calcium channel blocker (amlodipine), and compared them with the effect of an ACE inhibitor alone. Thirty hypertensive, type II diabetic patients with microalbuminuria were treated with either an ACE inhibitor alone (group I, n=17) or an ACE inhibitor plus amlodipine (group II, n=13) for 32 weeks. With treatment, blood pressures in both groups were significantly reduced, and diastolic blood pressure was lowered to a much greater extent in group II (76 +/- 2 mmHg) than in group I (83 +/- 2 mmHg, p < 0.05). Although the urinary albumin excretion rate was decreased in both groups, the decrease attained statistical significance only in group II (from 141 +/- 25 mg/day to 69 +/- 18 mg/day, p < 0.05); the extent of reduction in microalbuminuria during antihypertensive treatment was significantly greater in group II (50 +/- 10%) than in group I (14 +/- 13%, p < 0.05). In conclusion, this study showed that in hypertensive microalbuminuric type II diabetic patients, the combination of an ACE inhibitor plus amlodipine resulted in a more pronounced decreased in blood pressure (diastolic blood pressure <80 mmHg) and a greater reduction in urinary albumin excretion than did use of an ACE inhibitor alone. This combination strategy should thus be a more effective tool for obtaining optimal blood pressure control in patients with diabetic nephropathy.
Risk for immune-mediated graft dysfunction in liver transplant recipients with recurrent HCV infection treated with pegylated interferon.

BACKGROUND & AIMS Patients with recurrent hepatitis C virus infection treated with pegylated interferon (PEG) after liver transplantation can develop severe immune-mediated graft dysfunction (IGD) characterized by plasma cell hepatitis or rejection. METHODS We conducted a multicenter case-control study of 52 liver transplant recipients with hepatitis C to assess the incidence of, risk factors for, and outcomes of PEG-IGD. Data from each patient were compared with those from 2 matched patients who did not develop PEG-IGD (n = 104). We performed a multivariate analysis of risk factors and analyzed treatment and outcomes of graft dysfunction subtypes. RESULTS Overall incidence of PEG-IGD during a 10-year study period was 7.2%. Risk factors included no prior PEG therapy (odds ratio = 5.3; P < .0001), therapy with PEGα-2a (odds ratio = 4.7; P = .03), and immune features (mainly plasma cell hepatitis) on pre-PEG therapy liver biopsies (odds ratio = 3.9; P = .005). The PEG-IGD group had lower long-term patient (61.5% vs 91.3% of controls) and graft (38.5% vs 85.6% of controls) survival and higher rates of retransplantation (34.6% vs 6.7% of controls) (all, P < .0001), without increases in sustained virologic response. Variables associated with increased mortality included acute rejection as the PEG-IGD sub-type (hazard ratio [HR] = 2.4; P = .002), a high level of alkaline phosphatase at PEG initiation (HR = 1.003; P = .005), and lack of a sustained virologic response (HR = 3.3; P = .04). Variables associated with graft failure included a high level of alkaline phosphatase at PEG initiation (HR = 1.002; P = .04) and lack of a sustained virologic response (HR = 2.1; P = .04). CONCLUSIONS PEG-IGD has high morbidity and mortality and is not associated with increased rates of virologic response. It is important to avoid PEG therapy in liver transplant recipients with specific clinical, biochemical, and histologic risk factors for PEG-IGD.
Gifted Kids or Pushy Parents? Foreign Acquisitions and Plant Performance in Indonesia

This paper uses micro data from the Indonesian Census of Manufacturing to analyze the causal relationship between foreign ownership and plant productivity. To control for the possible endogeneity of the FDI decision, a difference-in-differences approach is combined with propensity score matching. An advantage of this method, which has not been previously applied in this context, is the ability to follow the timing of observed changes in productivity and other aspects of plant performance. The results suggest that foreign ownership leads to significant productivity improvements in the acquired plants. The improvements become visible in the acquisition year and continue in subsequent periods. After three years, the acquired plants outperform the control group in terms of productivity by 34 percentage points. The data also suggest that the rise in productivity is a result of restructuring, as acquired plants increase investment outlays, employment and wages. Foreign ownership also appears to enhance the integration of plants into the global economy through increased exports and imports.
The pharmacokinetics, safety and efficacy of tenofovir and emtricitabine in HIV-1-infected pregnant women

Objective:To describe the pharmacokinetics of tenofovir and emtricitabine in the third trimester of pregnant HIV-infected women and at postpartum. Design:A nonrandomized, open-label, multicentre phase IV study in HIV-infected pregnant women recruited from HIV treatment centres in Europe. Methods:HIV-infected pregnant women treated with the nucleotide/nucleoside analogue reverse transcriptase inhibitors (NRTIs) tenofovir disoproxil fumarate (TDF 300 mg; equivalent to 245 mg tenofovir disoproxil) and/or emtricitabine (FTC 200 mg) were included in the study. Twenty-four-hour pharmacokinetic curves were recorded in the third trimester (preferably week 33) and postpartum (preferably week 4–6). Collection of a cord blood sample and maternal sample at delivery was optional. Pharmacokinetic parameters were calculated using WinNonlin software version 5.3. Statistical analysis was conducted using SPSS version 16.0. Results:Thirty-four women were included in the analysis. Geometric mean ratios of third trimester vs. postpartum [90% confidence interval (CI)] were 0.77 (0.71–0.83) for TDF area under the curve (AUC0–24 h); 0.81 (0.68–0.96) for TDF Cmax and 0.79 (0.70–0.90) for TDF C24 h and 0.75 (0.68–0.82) for FTC AUC0–24 h; and 0.87 (0.77–0.99) for FTC Cmax and 0.77 (0.52–1.12) for FTC C24 h. The viral load close to delivery was less than 200 copies/ml in all but one patient, the average gestational age at delivery was 38 weeks. All children were tested HIV-negative and no congenital abnormalities were reported. Conclusion:Although pharmacokinetic exposure of the NRTIs TDF and FTC during pregnancy is approximately 25% lower, this was not associated with virological failure in this study and did not result in mother-to-child transmission.
Meteorite-catalyzed syntheses of nucleosides and of other prebiotic compounds from formamide under proton irradiation

Significance Modern research on the origin of life started with Urey–Miller’s 1953 report on the spontaneous formation of amino acids upon application of electric discharge on a model of the pristine Earth atmosphere. Formamide provides a chemically sound starting material for the syntheses of prebiotic compounds; its role in prebiotics is becoming recognized. Kiloparsecs-wide clouds of formamide were observed in the interstellar space. The energy sources for the syntheses explored so far were largely thermal, and the catalysts used were mostly terrestrial. In the presence of meteorites and with high-energy protons, we observe the production of unprecedented panels of nucleobases, sugars, and, most notably, nucleosides. Carboxylic acids and amino acids complete the recipe. These findings extend prebiotic plausible scenarios well beyond our planet. Liquid formamide has been irradiated by high-energy proton beams in the presence of powdered meteorites, and the products of the catalyzed resulting syntheses were analyzed by mass spectrometry. Relative to the controls (no radiation, or no formamide, or no catalyst), an extremely rich, variegate, and prebiotically relevant panel of compounds was observed. The meteorites tested were representative of the four major classes: iron, stony iron, chondrites, and achondrites. The products obtained were amino acids, carboxylic acids, nucleobases, sugars, and, most notably, four nucleosides: cytidine, uridine, adenosine, and thymidine. In accordance with theoretical studies, the detection of HCN oligomers suggests the occurrence of mechanisms based on the generation of radical cyanide species (CN·) for the synthesis of nucleobases. Given that many of the compounds obtained are key components of extant organisms, these observations contribute to outline plausible exogenous high-energy–based prebiotic scenarios and their possible boundary conditions, as discussed.
Super-Relaxed ()-Proximal Point Algorithms, Relaxed ()-Proximal Point Algorithms, Linear Convergence Analysis, and Nonlinear Variational Inclusions

We glance at recent advances to the general theory of maximal (set-valued) monotone mappings and their role demonstrated to examine the convex programming and closely related field of nonlinear variational inequalities. We focus mostly on applications of the super-relaxed ()-proximal point algorithm to the context of solving a class of nonlinear variational inclusion problems, based on the notion of maximal ()-monotonicity. Investigations highlighted in this communication are greatly influenced by the celebrated work of Rockafellar (1976), while others have played a significant part as well in generalizing the proximal point algorithm considered by Rockafellar (1976) to the case of the relaxed proximal point algorithm by Eckstein and Bertsekas (1992). Even for the linear convergence analysis for the overrelaxed (or super-relaxed) ()-proximal point algorithm, the fundamental model for Rockafellar's case does the job. Furthermore, we attempt to explore possibilities of generalizing the Yosida regularization/approximation in light of maximal ()-monotonicity, and then applying to first-order evolution equations/inclusions.
Transport Fitness of Cull Sows and Boars: A Comparison of Different Guidelines on Fitness for Transport

Simple Summary Breeding sows and boars that are shipped to slaughter, auctions, or buying stations have a greater risk for welfare problems because they are older animals. Sows are sold when they fail to rebreed, are too thin or have difficulty walking. The transport guidelines of four organizations were compared. Most guidelines typically do not allow transport of non-ambulatory, severely injured animals or sows likely to give birth. The guidelines were less likely to agree on transport of extremely thin sows. Abstract Sows and boars that have reached the end of their productive lives have a greater risk for welfare problems. This paper reviews literature on culling reasons that may affect the animals’ fitness for transport. The top two reasons identified for culling boars were: obesity and reproductive problems. Sows are most often culled due to lameness, low body condition, or failure to rebreed. The OIE (World Organization for Animal Health) fitness for transport guidelines that would apply to sows and boars were compared with documents from the Canadian Code of Practice, Northern American Meat Institute (NAMI), EU-UK-DEFRA (European Union-United Kingdom, Dept. Environment, Food and Rural Affairs), U.S. National Pork Board, European Practical Guidelines to Assess Fitness for Transport of Pigs, and U.S. Pork Trucker Quality Assurance. The guidelines had the greatest agreement on the following fitness for transport issues: non-ambulatory, severely injured animals, sows in the last ten percent of pregnancy and sows with uterine prolapses were not fit for transport. There was less agreement on low body condition. One of the reasons for the lack of agreement is that there were stakeholders who specialized in transporting and processing extremely thin animals. A standard that would severely restrict the transport and slaughter of these animals could hinder the business practices of these stakeholders. Many welfare specialists would agree that some of these animals would be unfit for transport.