Miracle-dz/UniFAR-FTUs huggingface dataset:
CALPAIN activity is increased in skeletal muscle from gastric cancer patients with no or minimal weight loss

The influence of cancer on skeletal muscle calpain expression and activity in humans is poorly understood. We tested the hypothesis that calpain activity is increased in skeletal muscle from gastric cancer patients with no or <5% weight loss. Muscle biopsies were obtained from rectus abdominis muscle in 15 patients who underwent surgery for gastric cancer and had <5% weight loss and also in 15 control patients. Calpain activity was determined using a calpain‐specific substrate in the absence or presence of calcium. The expression of μ‐ and m‐calpain, calpastatin, atrogin‐1, and MuRF1 was determined by real‐time polymerase chain reaction. Calpain activity was increased by 70% in cancer patients compared with controls. There were no differences in mRNA levels for μ‐ and m‐calpain, calpastatin, atrogin‐1, or MuRF1 between control and cancer patients. Calpain activity may be increased in muscle from gastric cancer patients even before changes in molecular markers of muscle wasting and significant weight loss occur. Muscle Nerve, 2011
Bilinear Generalized Approximate Message Passing—Part I: Derivation

In this paper, we extend the generalized approximate message passing (G-AMP) approach, originally proposed for high-dimensional generalized-linear regression in the context of compressive sensing, to the generalized-bilinear case, which enables its application to matrix completion, robust PCA, dictionary learning, and related matrix-factorization problems. Here, in Part I of a two-part paper, we derive our Bilinear G-AMP (BiG-AMP) algorithm as an approximation of the sum-product belief propagation algorithm in the high-dimensional limit, where central-limit theorem arguments and Taylor-series approximations apply, and under the assumption of statistically independent matrix entries with known priors. In addition, we propose an adaptive damping mechanism that aids convergence under finite problem sizes, an expectation-maximization (EM)-based method to automatically tune the parameters of the assumed priors, and two rank-selection strategies. In Part II of the paper, we will discuss the specializations of EM-BiG-AMP to the problems of matrix completion, robust PCA, and dictionary learning, and we will present the results of an extensive empirical study comparing EM-BiG-AMP to state-of-the-art algorithms on each problem.
The Effect of Cellular Differentiation on HSV-1 Infection of Oligodendrocytic Cells

Herpes simplex type 1 (HSV-1) is a neurotropic virus that infects many types of cells. Previous studies have demonstrated that oligodendrocytic cells are highly susceptible to HSV-1 infection. Here we analysed HSV-1 infection of a human oligodendrocytic cell line, HOG, and oligodendrocyte precursor cells (OPCs) cultured under growth or differentiation conditions. In addition to cell susceptibility, the role of the major cell receptors for viral entry was assessed. Our results revealed that OPCs and HOG cells cultured under differentiation conditions became more susceptible to HSV-1. On the other hand, viral infection induced morphological changes corresponding to differentiated cells, suggesting that HSV-1 might be inducing cell differentiation. We also observed colocalization of HVEM and nectin-1 with viral particles, suggesting that these two major HSV-1 receptors are functional in HOG cells. Finally, electron microscopy assays indicated that HSV-1 may be also entering OLs by macropinocytosis depending on their differentiation stage. In addition, vesicles containing intracellular enveloped virions observed in differentiated cells point to an endocytic mechanism of virus entry. All these data are indicative of diverse entry pathways dependent on the maturation stage of OLs.
Carbon isotope values in conodont elements from the latest Devonian–Early Carboniferous carbonate platform facies (Timan-Pechora Basin)

The δCorg values and their variations in conodont elements of the latest Famennian–Tournaisian species Polygnathus parapetus Druce are considered. The conodonts studied come from the latest Famennian–Tournaisian interval of the Kamenka River section (Timan-Pechora Basin). The carbon isotope composition of conodont elements had an average value of –25.2‰, suggesting a low trophic level of this species. During the latest Famennian (praesulcata conodont Zone) δCorg shifted to more negative values (up to –30.4‰), which may be attributed to changes in the global carbon cycle and local influx of organic matter of terrestrial origin during the terminal Famennian regression.
Human Aggression

Research on human aggression has progressed to a point at which a unifying framework is needed. Major domain-limited theories of aggression include cognitive neoassociation, social learning, social interaction, script, and excitation transfer theories. Using the general aggression model (GAM), this review posits cognition, affect, and arousal to mediate the effects of situational and personological variables on aggression. The review also organizes recent theories of the development and persistence of aggressive personality. Personality is conceptualized as a set of stable knowledge structures that individuals use to interpret events in their social world and to guide their behavior. In addition to organizing what is already known about human aggression, this review, using the GAM framework, also serves the heuristic function of suggesting what research is needed to fill in theoretical gaps and can be used to create and test interventions for reducing aggression.
Vitamin C Depletion and All-Cause Mortality in Renal Transplant Recipients

Vitamin C may reduce inflammation and is inversely associated with mortality in the general population. We investigated the association of plasma vitamin C with all-cause mortality in renal transplant recipients (RTR); and whether this association would be mediated by inflammatory biomarkers. Vitamin C, high sensitive C-reactive protein (hs-CRP), soluble intercellular cell adhesion molecule 1 (sICAM-1), and soluble vascular cell adhesion molecule 1 (sVCAM-1) were measured in a cohort of 598 RTR. Cox regression analyses were used to analyze the association between vitamin C depletion (≤28 µmol/L; 22% of RTR) and mortality. Mediation analyses were performed according to Preacher and Hayes’s procedure. At a median follow-up of 7.0 (6.2–7.5) years, 131 (21%) patients died. Vitamin C depletion was univariately associated with almost two-fold higher risk of mortality (Hazard ratio (HR) 1.95; 95% confidence interval (95%CI) 1.35–2.81, p < 0.001). This association remained independent of potential confounders (HR 1.74; 95%CI 1.18–2.57, p = 0.005). Hs-CRP, sICAM-1, sVCAM-1 and a composite score of inflammatory biomarkers mediated 16%, 17%, 15%, and 32% of the association, respectively. Vitamin C depletion is frequent and independently associated with almost two-fold higher risk of mortality in RTR. It may be hypothesized that the beneficial effect of vitamin C at least partly occurs through decreasing inflammation.
Comprehensive Arthroscopic Management of Glenohumeral Osteoarthritis: Preoperative Factors Predictive of Treatment Failure

Background: Patient selection is critical when choosing between arthroscopic joint preservation and total shoulder arthroplasty in young patients with glenohumeral osteoarthritis (GHOA). Purpose: To identify prognostic factors predictive of early failure in patients undergoing comprehensive arthroscopic management (CAM) for GHOA. Study Design: Case-control study; Level of evidence, 3. Methods: A total of 107 shoulders in 98 patients with minimum 2-year follow-up who underwent CAM were identified and evaluated. All shoulders met clinical and radiographic criteria for total shoulder arthroplasty (TSA), but the patients opted for joint preservation with arthroscopic management. Radiographic and preoperative factors were analyzed to determine predictors of early failure, defined as progression to TSA within the study period. Results: There were 72 men and 26 women with a mean age of 52 years (range, 29-77 years). Seventeen (15.8%) of 107 shoulders progressed to TSA at a mean of 2 years (range, 0.46-8.2 years). Shoulder status for the rest had a mean follow-up of 3.9 years (range, 2-9.4 years). There were a number of radiographic features that were correlated with early failure. Patients who failed had significantly less preoperative joint space than did those who succeeded (1.3 vs 2.6 mm; P = .004). Higher Kellgren-Lawrence grades for osteoarthritis and age older than 50 were also associated with failure. Shoulders with Walch type B2 and C glenoid were significantly more likely to fail than were Walch types A1, A2, and B1 (P < .05). Conclusion: The CAM procedure has been shown to reliably improve pain and function in active patients with advanced GHOA; however, it is important to inform patients about the limitations of the procedure. Patients with less joint space and abnormal posterior glenoid shape were significantly more likely to progress to early failure.
Altered expression of CYP in TSOD mice: a model of type 2 diabetes and obesity

To investigate the pharmacokinetic characteristics in TSOD (Tsumura, Suzuki, obese, diabetes) mice, a model of type 2 diabetes and obesity, the expressions of major hepatic CYP enzymes in TSOD and TSNO (Tsumura, Suzuki, non-obesity; control) mice were compared. The 7-month-old TSOD mice, which represented severe obesity/diabetes-related pathophysiology, showed higher expressions of Cyp2c and Cyp3a compared with TSNO mice, while those of Cyp1a and Cyp2e were lower. Cyp3a metabolic activity was also higher in TSOD mice. In the 7-month-old liver, pregnane X receptor (PXR) (nuclear receptor) and peroxisome proliferator-activated receptor-gamma coactivator-1alpha (PGC-1alpha) (cofactor) mRNA expression were higher in TSOD mice, possibly playing a role in the altered expression of Cyp3a. This specifically altered CYP expression in TSOD mice suggests that the biotransformation of drugs metabolized by these CYP enzymes differs from that in normal animals. Based on these findings, further investigation on the relationship between altered CYP expression and pathophysiology may be useful in elucidating changes in pharmacokinetics in obese/diabetic patients.
FAK mediates the activation of cardiac fibroblasts induced by mechanical stress through regulation of the mTOR complex.

AIMS Cardiac fibroblasts are activated by mechanical stress, but the underlying mechanisms involved remain poorly understood. In this study, we investigated whether focal adhesion kinase (FAK) plays a role in the activation of cardiac fibroblasts in response to cyclic stretch. METHODS AND RESULTS Neonatal (NF-P3/80--third passage, 80% confluence) and adult (AF-P1/80--first passage, 80% confluence) rat cardiac fibroblasts were exposed to cyclic stretch (biaxial, 1 Hz), which enhanced FAK phosphorylation at Tyr397. Proliferation (anti-5-bromo-2'-deoxyuridine and anti-Ki67 nuclear labelling), differentiation into myofibroblasts (expression of alpha-smooth muscle actin--alpha-SMA), and the activity of matrix metalloproteinase-2 were equally enhanced in stretched NF-P3/80 and AF-P1/80. Treatment with the integrin inhibitor RGD peptide impaired FAK phosphorylation and increased apoptosis (TUNEL) in non-stretched and stretched NF-P3/80, whereas FAK silencing induced by small interfering RNA modestly enhanced apoptosis only in stretched cells. RGD peptide or FAK silencing suppressed the activation of NF-P3/80 invoked by cyclic stretch. In addition, NF-P3/80 depleted of FAK were defective in AKT Ser473, TSC-2 Thr1462, and S6 kinase Thr389 phosphorylation induced by cyclic stretch. The activation of NF-P3/80 invoked by cyclic stretch was prevented by pre-treatment with the mammalian target of rapamycin (mTOR) inhibitor rapamycin, whereas supplementation with the amino acid, leucine, activated S6K and rescued the stretch-induced activation of NF-P3/80 depleted of FAK. CONCLUSIONS These findings demonstrate a critical role for the mTOR complex, downstream from FAK, in mediating the activation of cardiac fibroblasts in response to mechanical stress.
Reinforcement Learning Dynamics in Social Dilemmas

In this paper we replicate and advance Macy and Flache's (2002; Proc. Natl. Acad. Sci. USA, 99, 7229â€“7236) work on the dynamics of reinforcement learning in 2×2 (2-player 2-strategy) social dilemmas. In particular, we provide further insight into the solution concepts that they describe, illustrate some recent analytical results on the dynamics of their model, and discuss the robustness of such results to occasional mistakes made by players in choosing their actions (i.e. trembling hands). It is shown here that the dynamics of their model are strongly dependent on the speed at which players learn. With high learning rates the system quickly reaches its asymptotic behaviour; on the other hand, when learning rates are low, two distinctively different transient regimes can be clearly observed. It is shown that the inclusion of small quantities of randomness in players' decisions can change the dynamics of the model dramatically.
Modeling Driver Behavior in a Cognitive Architecture

Objective: This paper explores the development of a rigorous computational model of driver behavior in a cognitive architecture--a computational framework with underlying psychological theories that incorporate basic properties and limitations of the human system. Background: Computational modeling has emerged as a powerful tool for studying the complex task of driving, allowing researchers to simulate driver behavior and explore the parameters and constraints of this behavior. Method: An integrated driver model developed in the ACT-R (Adaptive Control of Thought-Rational) cognitive architecture is described that focuses on the component processes of control, monitoring, and decision making in a multilane highway environment. Results: This model accounts for the steering profiles, lateral position profiles, and gaze distributions of human drivers during lane keeping, curve negotiation, and lane changing. Conclusion: The model demonstrates how cognitive architectures facilitate understanding of driver behavior in the context of general human abilities and constraints and how the driving domain benefits cognitive architectures by pushing model development toward more complex, realistic tasks. Application: The model can also serve as a core computational engine for practical applications that predict and recognize driver behavior and distraction.
The UKA/CMU statistical machine translation system for IWSLT 2006

In this paper we describe the CMU statistical machine translation system used in the IWSLT 2005 evaluation campaign. This system is based on phrase-to-phrase translations extracted from a bilingual corpus. We experimented with two different phrase extraction methods; PESA on-the-fly phrase extraction and alignment free extraction method. The translation model, language model and other features were combined in a log-linear model during decoding. We present our experiments on model adaptation for new data in a different domain, as well as combining different translation hypotheses to obtain better translations. We participated in the supplied data track for manual transcriptions in the translation directions: ArabicEnglish, Chinese-English, Japanese-English and KoreanEnglish. For Chinese-English direction we also worked on ASR output of the supplied data, and with additional data in unrestricted and C-STAR tracks.
Ridge Preservation for Implant Therapy: a Review of the Literature

Healing of the extraction socket after tooth removal involves retention of the blood clot followed by a sequence of events that lead to changes in the alveolar process in a three dimensional fashion. This normal healing event results in a minimal loss of vertical height (around 1 mm), but a substantial loss of width in the buccal-lingual plane (4-6 mm). During the first three months following extraction that loss has been shown to be significant and may result in both a hard tissue and soft tissue deformity affecting the ability to restore the site with acceptable esthetics. Procedures that reduce the resorptive process have been shown to be predictable and potentially capable of eliminating secondary surgery for site preparation when implant therapy is planned. The key element is prior planning by the dental therapist to act at the time of extraction to prevent the collapse of the ridge due to the loss of the alveolus. Several techniques have been employed as ridge preservation procedures involving the use of bone grafts, barrier membranes and biologics to provide a better restorative outcome. This review will explore the evidence behind each technique and their efficacy in accomplishing site preparation. The literature does not identify a single technique as superior to others; however, all accepted therapeutic procedures for ridge preservation have been shown to be more effective than blood clot alone in randomized controlled studies.
Development and comparison of a generic multiple‐locus variable‐number tandem repeat analysis with pulsed‐field gel electrophoresis for typing of Salmonella enterica subsp. enterica

Salmonella enterica subsp. enterica causes salmonellosis in humans and animals. Serovar‐specific multiple‐locus variable‐number tandem repeat analysis (MLVA) is widely used for Salmonella surveillance; however, isolates have to be serotyped prior to MLVA typing and only the most common serovars can be typed. We developed a MLVA scheme for high‐discriminatory typing of Salmonella.
Cortical Venous Filling on Dynamic Computed Tomographic Angiography: A Novel Predictor of Clinical Outcome in Patients With Acute Middle Cerebral Artery Stroke

Background and Purpose— Venous flow in the downstream territory of an occluded artery may influence patient prognosis after ischemic stroke. Our aim was to study cortical venous filling (CVF) in a time-resolved manner with dynamic computed tomographic angiography and to assess the relationship with clinical outcome. Methods— Patients with a proximal middle cerebral artery occlusion underwent noncontrast CT and whole-brain CT perfusion/dynamic CT angiography within 9 hours after stroke-onset. We defined poor outcome as a modified Rankin Scale score of ≥3. Association between the extent and velocity of CVF and poor outcome at 3 months was analyzed with Poisson-regression. Prognostic value of optimal CVF (maximum opacification of cortical veins) in addition to age, stroke severity, treatment, Alberta Stroke Program Early CT score, cerebral blood flow, and collateral status was assessed with logistic regression and summarized with the area under the curve. Results— Eighty-eight patients were included, with a mean age of 67 years. By combining the extent and velocity of optimal CVF, we observed a decreased risk of poor outcome in patients with good and fast optimal CVF, risk ratio of 0.5 (95% confidence interval, 0.3–0.7). Extent and velocity of optimal CVF had additional prognostic value (area under the curve, 0.88; 95% confidence interval, 0.77–0.98; P<0.02) compared with a model without CVF information. Conclusions— The combination of extent and velocity of optimal CVF, as assessed with dynamic CT angiography, is useful to identify patients with acute middle cerebral artery stroke at higher risk of poor clinical outcome at 3-month follow-up. Clinical Trial Registration— URL: http://www.trialregister. nl/trialreg and http://www.clinicaltrials. gov. Unique identifier: NTR1804 and NCT00880113, respectively.
Near-field antenna measurements using nonideal measurement locations

We introduce a near-field to far-field transformation algorithm that relaxes the usual restriction that data points be located on a plane rectangular grid. Computational complexity is O(Nlog N) where N is the number of data points. This algorithm allows efficient processing of near-field data with known probe position errors. Also, the algorithm is applicable to other measurement approaches such as plane-polar scanning, where data are collected intentionally on a nonrectangular grid.
A Latent Discriminative Model for Compositional Entailment Relation Recognition using Natural Logic

Recognizing semantic relations between sentences, such as entailment and contradiction, is a challenging task that requires detailed analysis of the interaction between diverse linguistic phenomena. In this paper, we propose a latent discriminative model that unifies a statistical framework and a theory of Natural Logic to capture complex interactions between linguistic phenomena. The proposed approach jointly models alignments, their local semantic relations, and a sentence-level semantic relation, and has hidden variables including alignment edits between sentences and their semantic relations, only requires sentences pairs annotated with sentence-level semantic relations as training data to learn appropriate alignments. In evaluation on a dataset including diverse linguistic phenomena, our proposed method achieved a competitive results on alignment prediction, and significant improvements on a sentence-level semantic relation recognition task compared to an alignment supervised model. Our analysis did not provide evidence that directly learning alignments and their labels using gold standard alignments contributed to semantic relation recognition performance and instead suggests that they can be detrimental to performance if used in a manner that prevents the learning of globally optimal alignments.
Metabolism and disposition of moxonidine in Fischer 344 rats.

The metabolism and disposition of moxonidine (4-chloro-5-(imidazolidin-2-ylidenimino)-6-methoxy-2-methylp yrimidine ), a potent central-acting antihypertensive agent, were investigated in F344 rats. After an i.v. or oral administration of 0.3 mg/kg of [(14)C]moxonidine, the maximum plasma concentrations of moxonidine were determined to be 146.0 and 4.0 ng/ml, respectively, and the elimination half-lives were 0.9 and 1.1 h, respectively. The oral bioavailability of moxonidine was determined to be 5.1%. The metabolic and elimination profiles of moxonidine were determined after an oral administration of 5 mg/kg of [(14)C]moxonidine. More than fifteen phase I and phase II metabolites of moxonidine were identified in the different biological matrices (urine, plasma, and bile). Oxidative metabolism of moxonidine leads to the formation of hydroxymethyl moxonidine and a carboxylic acid metabolite as the major metabolites. Several GSH conjugates, cysteinylglycine conjugates, cysteine conjugates, and a glucuronide conjugate were also identified in rat bile samples. The radiocarbon was eliminated primarily by urinary excretion in rats, with 59.5% of total radioactivity recovered in the urine and 38.4% recovered in the feces within 120 h. In bile duct-cannulated rats, about 39.7% of the radiolabeled dose was excreted in the urine, 32.6% excreted in the bile, and approximately 2% remained in the feces. The results from a quantitative whole body autoradiography study indicate that radiocarbon associated with [(14)C]moxonidine and/or its metabolites was widely distributed to tissues, with the highest levels of radioactivity observed in the kidney and liver. In summary, moxonidine is well absorbed, extensively metabolized, widely distributed into tissues, and rapidly eliminated in rats after oral administration.