Miracle-dz/UniFAR-FTUs huggingface dataset:
Documented deaths of hepatic lobe donors for living donor liver transplantation

The actual risk of death in hepatic lobe donors for living donor liver transplantation (LDLT) is unknown because of the lack of a comprehensive database. In the absence of a definitive estimate of the risk of donor death, the medical literature has become replete with anecdotal reports of donor deaths, many of which cannot be substantiated. Because donor death is one of the most important outcomes of LDLT, we performed a comprehensive survey of the medical and lay literature to provide a referenced source of worldwide donor deaths. We reviewed all published articles from the medical literature on LDLT and searched the lay literature for donor deaths from 1989 to February 2006. We classified each death as “definitely,” “possibly,” or “unlikely” related to donor surgery. We identified 19 donor deaths (and one additional donor in a chronic vegetative state). Thirteen deaths and the vegetative donor were “definitely,” 2 were “possibly,” and 4 were “unlikely” related to donor surgery. The estimated rate of donor death “definitely” related to donor surgery is 0.15%. The rate of donor death which is “definitely” or “possibly” related to the donor surgery is 0.20%. This analysis provides a source document of all identifiable living liver donor deaths, provides a better estimate of donor death rate, and may provide an impetus for centers with unreported deaths to submit these outcomes to the liver transplantation community. Liver Transpl 12:1485‐1488, 2006. © 2006 AASLD.
Measuring Enzymatic HIV-1 Susceptibility to Two Reverse Transcriptase Inhibitors as a Rapid and Simple Approach to HIV-1 Drug-Resistance Testing

Simple and cost-effective approaches for HIV drug-resistance testing are highly desirable for managing increasingly expanding HIV-1 infected populations who initiate antiretroviral therapy (ART), particularly in resource-limited settings. Non-nucleoside reverse trancriptase inhibitor (NNRTI)-based regimens with an NRTI backbone containing lamivudine (3TC) or emtricitabine (FTC) are preferred first ART regimens. Failure with these drug combinations typically involves the selection of NNRTI- and/or 3TC/FTC- resistant viruses. Therefore, the availability of simple assays to measure both types of drug resistance is critical. We have developed a high throughput screening test for assessing enzymatic resistance of the HIV-1 RT in plasma to 3TC/FTC and NNRTIs. The test uses the sensitive “Amp-RT” assay with a newly-developed real-time PCR format to screen biochemically for drug resistance in single reactions containing either 3TC-triphosphate (3TC-TP) or nevirapine (NVP). Assay cut-offs were defined based on testing a large panel of subtype B and non-subtype B clinical samples with known genotypic profiles. Enzymatic 3TC resistance correlated well with the presence of M184I/V, and reduced NVP susceptibility was strongly associated with the presence of K103N, Y181C/I, Y188L, and G190A/Q. The sensitivity and specificity for detecting resistance were 97.0% and 96.0% in samples with M184V, and 97.4% and 96.2% for samples with NNRTI mutations, respectively. We further demonstrate the utility of an HIV capture method in plasma by using magnetic beads coated with CD44 antibody that eliminates the need for ultracentifugation. Thus our results support the use of this simple approach for distinguishing WT from NNRTI- or 3TC/FTC-resistant viruses in clinical samples. This enzymatic testing is subtype-independent and can assist in the clinical management of diverse populations particularly in resource-limited settings.
Effect of dietary combinations on plaque pH recovery after the intake of pediatric liquid analgesics

Objectives:To study the effect of water, halloumi cheese and sugar-free (SF) chewing gum on plaque pH recovery after the intake of sweetened PLAs. Settings and Design: A randomized clinical trial was conducted on 17 children (10 females, 7 males) aged 11–12 years with DFT/dft of more than 3. Materials and Methods:Each volunteer tested paracetamol and ibuprofen suspension alone or followed with water, halloumi cheese or SF gum, as well as 10% sucrose and 10% sorbitol as controls. Plaque pH was measured using the sampling method before and after 5, 10, 15, 20, 30 min of ingestion. Statistical Analysis:Statistical analysis was performed using analysis of variance followed by least significant difference test to assess minimum pH (min pH), maximum pH drop (ΔpH), and the area under baseline pH, and P value was set as 0.05. Results:Both ibuprofen and paracetamol were not significantly different from 10% sucrose in terms of min pH, ΔpH, and area under baseline pH except for min pH of ibuprofen (P = 0.034). Water and halloumi cheese did not have a significant effect on plaque pH recovery after the intake of both analgesics as min pH, ΔpH, and area under baseline pH were similar to 10% sucrose except for min pH of ibuprofen + water (P = 0.048). However, plaque pH variables after chewing SF gum for 20 min were similar to 10% sorbitol. Conclusion:Chewing SF gum immediately after the intake of sweetened PLAs for 20 min restores plaque pH and could be recommended as a complementary aid in caries prevention.
Repetitive administration of Shaoyao‐Gancao‐tang to rats restores the bioavailability of glycyrrhizin reduced by antibiotic treatment

Shaoyao‐Gancao‐tang (SGT), a traditional Chinese formulation, is often used together with antibiotics such as amoxicillin and metronidazole (AMPC‐MET) for the treatment of peptic ulcers in Japan. However, the bioavailability of glycyrrhizin (GL) in SGT is severely reduced by a single administration of AMPC‐MET, and the reducing effect continues for 12 days. GL is one of the major pharmacologically important glycosides in SGT and is transformed into the active metabolite 18β‐glycyrrhetic acid (GA) by intestinal bacteria in the gut, followed by absorption of the latter into the blood. In order to reduce the negative effect of AMPC‐MET on the bioavailability of GL, the optimum scheduling of the medications was examined. We found that the reduction in the plasma GA concentration and the GL‐metabolizing activity in faeces caused by a single dose of AMPC‐MET could be sharply attenuated by the repetitive administration of SGT for 4 days. The GA concentration and the GL‐metabolizing activity were strongly enhanced by further continuous administration of SGT. These findings suggest that repetitive administration of SGT starting 1 or 2 days after the administration of AMPC‐MET speeds the recovery of the bioavailability of GL in SGT. Similar strategies for administering medications may also be useful for combination therapy of antibiotics with other traditional Chinese formulations containing bioactive glycosides.
[Clinical features of pyogenic liver abscess according to age group].

BACKGROUND/AIMS Pyogenic liver abscess remains a major diagnostic and therapeutic challenge, despite advances in diagnostic technology and new strategies for treatment. This study was conducted to compare the differences in clinical features and outcomes of pyogenic liver abscess according to age. METHODS In total, 166 patients were enrolled and included 63 (<65 years old, group I), 62 (65-74 years old, group II), 41 (>75 years old, group III) patients in each group. We reviewed the medical records retrospectively including etiology, underlying diseases, characteristics of the liver abscess, laboratory and microbiologic findings, treatment, and outcome of the patients. RESULTS Group I had higher prevalence rates of male patients and chronic alcoholics, but lower prevalence rates of biliary disease, hypertension, and malignancy. In laboratory findings, group II had higher incidence of thrombocytopenia, elevated blood urea nitrogen and creatinine. There were no differences in symptoms and microbiologic findings in blood and pus among the three groups. Liver abscesses were more common in right liver in Group I. The lengths of stay and the treatment modalities were similar in three groups. CONCLUSIONS Although there were differences in sex ratio, etiology, underlying disease among the different age groups, they did not cause difference in treatment and clinical outcome of pyogenic liver abscess. Thus, we recommend active treatments in patients of all age.
Taxonomic Classification for Living Organisms Using Convolutional Neural Networks

Taxonomic classification has a wide-range of applications such as finding out more about evolutionary history. Compared to the estimated number of organisms that nature harbors, humanity does not have a thorough comprehension of to which specific classes they belong. The classification of living organisms can be done in many machine learning techniques. However, in this study, this is performed using convolutional neural networks. Moreover, a DNA encoding technique is incorporated in the algorithm to increase performance and avoid misclassifications. The algorithm proposed outperformed the state of the art algorithms in terms of accuracy and sensitivity, which illustrates a high potential for using it in many other applications in genome analysis.
Towards a Tool Supporting Integration Testing of Aspect-Oriented Programs

Aspect-Oriented Programming is an emerging software engineering paradigm. It offers new constructs and tools improving separation of crosscutting concerns into single units called aspects. AspectJ, the most used aspect-oriented programming language, represents an extension of Java. In fact, existing object-oriented programming languages suffer from a serious limitation in modularizing adequately crosscutting concerns in a program. Many concerns crosscut several classes in an object-oriented system. However, new dependencies between aspects and classes result in new testing challenges. Interactions between aspects and classes are new sources for program faults. Moreover, existing object-oriented testing methods (unit and integration testing) are not well adapted to the aspect technology. As a consequence, new testing techniques must be developed for aspect-oriented programs. We present, in this paper, a new aspects-classes integration testing strategy and the associated tool. The adopted approach consists of two main phases: (1) static analysis: generating testing sequences based on dynamic interactions between aspects and classes, (2) dynamic analysis: verifying the execution of the selected sequences. We focus, in particular, on the integration of one or more aspects in the control of collaborating classes.
Eicosanoid and cytokine levels in plasma of patients during mesenteric infarction

Multible organ failure (MOF) induced by mesenteric infarction is associated with a high mortality rate. This study reports eicosanoid and cytokine levels in the blood of three atherosclerotic patients who ultimately died from MOF induced by mesenteric infarction. High plasma levels of 6- keto-prostaglandin (PG) F1α (the stable metabolite of PGI2), interleukin (IL)-6 and IL-8 are observed whereas plasma tumour necrosis factor alpha (TNFα), TxB2 (the stable metabolite of TxA2), PGE2, leukotrienes (LT)B4 and LTC4, and whole blood platelet-activating factor levels are not different from values obtained in similarly severe atherosclerotic patients. This short report questioned the clinical involvement of TNFα during such a pathology where a persistent translocation of endotoxin has been observed through the gut endothelial barrier. Activation of phospholipase A2 is suggested by the increase in the stable metabolite of PGI2 and might be by itself or through lipidic metabolites, a major systemic stimulus of IL-6 and IL-8 production.
Comparison of DAS-ELISA and RT-PCR Methods for the Detection of Prunus Necrotic Ringspot Virus (PNRSV)

Two methods (DAS-ELISA and RT-PCR) were compared for the detection of Prunus necrotic ringspot virus (PNRSV) in woody host Prunus mahleb isolated from Malatya. Total RNA extractions were made from serially diluted fresh leaf tissue, root, bark and one year old green bark tissue using silica-based method. Purified total RNA extracts were used as template for cDNA synthesis by reverse transcription. PCR products, about 616 base pair in size, was analyzed by gel electrophoresis and visualized by ethidium bromide staining. Comparing ELISA test, RT-PCR was found more sensitive in detecting local PNRSV isolate. Several plant tissues were used for the evaluation of best tissue in the detection of PNRSV by RT-PCR. Leaf tissue of infected P. mahaleb was proved to be more suitable tissue in detection of virus by RT-PCR respect to root, one-year-old green bark tissue and bark tissue.
Effect of bed roughness on the propagation of negative surges in rivers and estuaries

In an open channel, a sudden drop in water elevation is associated with a negative surge. Practical applications include the ebb tide motion in estuaries with macro-tidal conditions, the rundown of the swash, and the retreat of tsunami waters after reaching the maximum runup. Herein a physical study is presented with a focus on the effects of bed roughness. Detailed measurements were performed in a large facility with three roughness types. The results are presented and practical applications are discussed. Mots clefs : Ondes négatives, Rugosité de fond, Ecoulements à surface libre, Ecoulement instationnaire
Horovitz containing TCP-1 Nested allosteric interactions in the cytoplasmic chaperonin

Initial rates of ATP hydrolysis by the chaperonin containing TCP-1 (CCT) from bovine testis were measured as a function of ATP concentration. Two allosteric transitions are observed: one at relatively low concentrations of ATP (<100 M) and the second at higher concentrations of ATP. The data suggest that CCT has positive intra-ring cooperativity and negative inter-ring cooperativity in ATP hydrolysis, with respect to ATP, as previously observed in the case of GroEL. It is shown that the relatively weak positive intra-ring cooperativity found in the case of CCT may be due to heterogeneity in its subunit composition. Our results suggest that nested allosteric behavior may be common to chaperone double-ring systems.
Epigenetic silencing of TIMP4 in heart failure

Tissue inhibitor of matrix metalloprotease 4 (TIMP4) is endogenously one of the key modulators of matrix metalloprotease 9 (MMP9) and we have reported earlier that cardiac specific TIMP4 instigates contractility and helps in differentiation of cardiac progenitor cells. Although studies show that the expression of TIMP4 goes down in heart failure but the mechanism is unknown. This study aims to determine the mechanism of silencing of TIMP4 in heart failure progression created by aorta‐vena cava (AV) fistula. We hypothesize that there is epigenetic silencing of TIMP4 in heart failure. To validate this hypothesis, we created heart failure model by creating AV fistula in C57BL/6 mice and looked into the promoter methylation (methylation specific PCR, high resolution melting, methylation sensitive restriction enzyme and Na bisulphite treatment followed by sequencing), histone modification (ChIP assay) and microRNAs that regulate TIMP4 (mir122a) and MMP9 (mir29b and mir455‐5p). The physiological parameters in terms of cardiac function after AV fistula were assessed by echocardiography. We observed that there are 7 CpG islands in the TIMP4 promoter which get methylated during the progression of heart failure which leads to its epigenetic silencing. In addition, the up‐regulated levels of mir122a in part, contribute to regulation of TIMP4. Consequently, MMP9 gets up‐regulated and leads to cardiac remodeling. This is a novel report to explain the epigenetic silencing of TIMP4 in heart failure.
Comparing and combining software defect detection techniques: a replicated empirical study

This report describes an empirical study comparing three defect detection techniques: a) code reading by stepwise abstraction, b) functional testing using equivalence partitioning and boundary value analysis, and c) structural testing using branch coverage. It is a replication of a study that has been carried out at least four times previously over the last 20 years. This study used 47 student subjects to apply the techniques to small C programs in a fractional factorial experimental design. The major findings of the study are: a) that the individual techniques are of broadly similar effectiveness in terms of observing failures and finding faults, b) that the relative effectiveness of the techniques depends on the nature of the program and its faults, c) these techniques are consistently much more effective when used in combination with each other. These results contribute to a growing body of empirical evidence that supports generally held beliefs about the effectiveness of defect detection techniques in software engineering.
Writing in a role for structure: low-income young people's dual understanding of agency, choice and the welfare state

ABSTRACT Young people, it is often argued, are more individualised and more free of older, class constraints than ever before. This has led some thinkers to debate the (positive) possibilities of ‘choice biographies’ and self-making among the young, alongside the (more sinister) possibilities of ‘epistemological fallacies’ blinding them to the limits of these self-making capacities. This article interrogates the idea of ‘epistemological fallacies’ for five groups of young people from low-income backgrounds in England. Comparing focus group discussions they had about their lives, with policies they wrote to address the problems of their lives, this article suggests that these young people were less blind to the limits of their own agency than individualisation theorists may predict, and were in fact acutely aware of the difficulties behind finding personal solutions to social problems.
Parametric macromodels of digital I/O ports

Addresses the development of macromodels for input and output ports of a digital device. The proposed macromodels consist of parametric representations that can be obtained from port transient waveforms at the device ports via a well established procedure. The models are implementable as SPICE subcircuits and their accuracy and efficiency are verified by applying the approach to the characterization of transistor-level models of commercial devices.
Paclitaxel induces apoptosis via protein kinase A- and p38 mitogen-activated protein-dependent inhibition of the Na+/H+ exchanger (NHE) NHE isoform 1 in human breast cancer cells.

PURPOSE The molecular signal components essential to paclitaxel-dependent apoptosis in breast cancers are potential targets for combined therapy. However, the signal mechanisms underlying paclitaxel action still need to be better defined. EXPERIMENTAL DESIGN In a breast cancer cell line, pharmacological agents and transient transfection with dominant interfering and constitutive active mutants were used to identify the signal transduction module involved in the regulation of paclitaxel-induced apoptosis and to evaluate its potential as a therapeutic target. RESULTS In MDA-MB-435 cells, paclitaxel treatment stimulated the activity of both protein kinase A and p38, and inhibited the activity of the Na(+)/H(+) exchanger isoform 1 (NHE1) with similar IC(50) concentrations as for its activation of apoptosis. Activation and inhibition experiments demonstrated that protein kinase A and p38 participate sequentially upstream of the NHE1 in regulating the paclitaxel-induced apoptotic pathway. Importantly, concurrent specific inhibition of the NHE1 with paclitaxel treatment resulted in a synergistic induction of apoptosis and a reduction in the paclitaxel IC(50) for apoptosis. This sensitization of paclitaxel apoptotic action by specific inhibition of NHE1 was verified in breast cancer cell lines with different paclitaxel sensitivity. CONCLUSIONS We have, for the first time, identified NHE1 as an essential component of paclitaxel-induced apoptosis in breast cancer cells and, importantly, identified that simultaneous inhibition of the NHE1 results in a synergistic potentiation of low-dose paclitaxel apoptotic action. As specific NHE1 inhibitors have finished Phase II/Phase III clinical trials for myocardial protection, there is the possibility for a rapid biological translation of this novel therapeutic strategy to a clinical setting.
"It might be nice to be a girl... Then you wouldn't have to be emotionless": Boys' resistance to norms of masculinity during adolescence

This article examines the patterns of resistance to norms of masculinity (i.e., emotional stoicism, physical toughness, and autonomy) and its association to psychological and social adjustment among boys from preadolescence through late adolescence. Semi-structured interviews were conducted longitudinally with a sample of 55 White, Black, Latino, and Chinese American boys from 6th grade to 11th grade. Our analyses indicated that boys’ resistance to norms of masculinity is explicit and implicit and is prevalent during adolescence, with 78% of the boys in our study demonstrating moderate to high levels of resistance typically during the middle school years. Four trajectories of resistance over time were detected: (a) decreasing resistance; (b) stable moderate-to-high levels of resistance; (c) stable low levels of resistance; and (d) mixed patterns of resistance. White, Black, and Chinese American boys were the most likely to suggest a decline in resistance from preto late adolescence, whereas the Latino boys were the least likely to suggest such a decline and the most likely to suggest stable moderate-to-high levels of resistance throughout adolescence. Findings suggest that resistance to norms of masculinity enhances psychological and social adjustment for boys during adolescence and is deeply influenced by the context in which boys are embedded.
Political Values, Culture, and Corporate Litigation

Using one of the largest samples of litigation data available to date, we examine whether the political culture of a firm determines its propensity for corporate misconduct. We measure political culture using the political contributions of top managers, firm political action committees, and local residents. We show that firms with a Republican culture are more likely to be the subject of civil rights, labor, and environmental litigation than are Democratic firms, consistent with the Democratic ideology that emphasizes equal rights, labor rights, and environmental protection. However, firms with a Democratic culture are more likely to be the subject of litigation related to securities fraud and intellectual property rights violations than are Republican firms, whose party ideology stresses self-reliance, property rights, market discipline, and limited government regulation. Upon litigation filing, both types of firms experience similar announcement reaction, which suggests that the observed relationship between political culture and corporate misconduct is unlikely to reflect differences in expected litigation costs.Data, as supplemental material, are available at http://dx.doi. org/10.1287/mnsc.2014. 2106 . This paper was accepted by Brad Barber, finance .
Optimization of the time-dependent traveling salesman problem with Monte Carlo methods.

A problem often considered in operations research and computational physics is the traveling salesman problem, in which a traveling salesperson has to find the shortest closed tour between a certain set of cities. This problem has been extended to more realistic scenarios, e.g., the "real" traveling salesperson has to take rush hours into consideration. We will show how this extended problem is treated with physical optimization algorithms. We will present results for a specific instance of Reinelt's library TSPLIB95, in which we define a zone with traffic jams in the afternoon.