Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV RNA and CD4 cell count response to protease inhibitor therapy in an urban AIDS clinic: response to both initial and salvage therapy.

OBJECTIVE To determine the HIV RNA and CD4 cell response to both initial and salvage therapy with protease inhibitor-based therapy, and to examine the relationship between the virological response and pre-therapy characteristics. DESIGN Observational cohort. SETTING University-based public hospital AIDS clinic. PATIENTS HIV-infected adults who received at least 16 continuous weeks' therapy with a potent protease inhibitor (indinavir, ritonavir or nelfinavir)-based regimen, and who have had at least 48 weeks of follow-up. MAIN OUTCOME MEASURES Plasma HIV RNA and CD4 cell count response at week 48 of therapy for patients receiving their first protease inhibitor-containing regimen, and at week 24 of therapy with a salvage regimen. RESULTS Of the 337 patients analysed, 170 (50.2%) had a successful outcome (HIV RNA <500 copies/ml after 48 weeks of treatment). Independent predictors of virological failure were higher baseline HIV RNA level, lower baseline CD4 cell count and failure to initiate at least one new nucleoside analog simultaneously at the time protease inhibitor therapy was initiated. The risk of failure increased incrementally across most HIV RNA and CD4 cell strata, with significant increases as the HIV RNA increased above 4.5 log10 copies/ml and the CD4 cell count fell below 100 cells/mm3 (P< or =0.01). The CD4 cell count remained above baseline to week 48 in most patients, regardless of the HIV RNA response. Of the 99 patients who experienced virological failure and switched to a salvage regimen, only 22 (22%) achieved an undetectable HIV RNA level 24 weeks after initiating salvage therapy. Independent predictors of failure with salvage therapy included an HIV RNA greater than 4.0 log10 RNA copies/ml at the time of the switch and failure to use a non-nucleoside reverse transcriptase inhibitor (NNRTI) in the salvage regimen. CONCLUSION Failure of potent protease inhibitor therapy to suppress HIV RNA levels below detectable levels is common in clinical practice, and can often be explained by their suboptimal use. CD4 T cell counts remain above baseline for at least one year in most patients experiencing virological failure. Successful salvage therapy, which was uncommon, was associated with a low plasma HIV RNA at the time of the switch and the use of a new class of antiretroviral agents (NNRTI) in the salvage regimen.
Does e-HRM improve labour productivity? A study of commercial bank workplaces in Pakistan

Drawing on data from a unique, large-scale survey, the purpose of this paper is to examine the links between e-HRM and perceived labour productivity both directly and through the mediating role of HR service quality amongst commercial-bank workplaces in Pakistan, many of which have introduced e-HRM. ,The authors use partial least squares structural equation modelling to examine the direct links between e-HRM and productivity as well as the mediated links between e-HRM, perceived HR service quality and productivity. ,The authors show that e-HRM practices have a statistically significant, positive effect on managers’ perceptions of labour productivity. The authors also reveal that e-HRM practices influence the quality of HR service, and that the quality of HR services fully mediates the relationship between e-HRM practices and managers’ perceptions of labour productivity. ,The results highlight the importance of designing and implementing e-HRM systems so that they support organisation workflow and enable workers to carry out a range of HR and non-HR activities more efficiently. In particular, this study suggests that managers should focus on how e-HRM impacts on HR service quality in a holistic way, as this is the “route” via which e-HRM can improve labour productivity. ,Existing research has demonstrated a link between e-HRM and the quality of HR services; however, these studies downplay the potential impact of e-HRM on labour productivity, a key organisational outcome and one that e-HRM aims to improve. This study contributes to the HRM literature by identifying how e-HRM can improve labour productivity by enhancing the perceived HR service quality. This study, therefore, provides the basis for future theory developments in this area.
Study of Passive Q-switch Mode-Locked Characteristic of Pulse LD Pump Nd: YVO4/Cr4+:YAG

Mode-locked characteristic in different cavity length and pump power has been compared in experiments and the main factors which affect the mode-locking have been discussed. By analysing the experimental results, the author gets the following conclusion: we can realize the Q-switch mode-locked laser output by using pulse LD pump Nd:YVO4/Cr4+:YAG. When the cavity length is shorter, we can only realize the Q-switch laser output, as cavity length and power density increase, we realize the Q-switch mode-locked laser output. The best mode-locked state reaches when cavity length is 170mm. As Cavity length is 190mm, due to thermal effects, mode-locking becomes unstable.
Autoinduction of the ompR response regulator by acid shock and control
 of the Salmonella enterica acid tolerance response

Salmonella enterica serovar Typhimurium periodically experiences acid stress in a variety of host and non‐host environments. An encounter with non‐lethal acid stress (pH > 4) induces an assortment of physiological changes, called the acid tolerance response (ATR), that helps the cell to tolerate extreme low pH (pH 3). These physiological changes differ in log phase and stationary phase cells and are controlled by different regulatory proteins. OmpR is an acid‐induced response regulator critical to the stationary phase ATR but not to the log phase ATR. As OmpR also controls the expression of the acid‐induced viru‐lence operon ssrAB, acid shock induction of ompR was examined to gain insight into how Salmonella links virulence with survival at extreme acid pH. The results indicate that acid pH induces ompR from a promoter different from that used for basal expression. Transcription from this promoter is repressed by the histone‐like protein H‐NS and requires OmpR‐P for induction. The classic sensor kinase EnvZ and acetyl phosphate collaborate to produce the optimum level of OmpR‐P needed for autoinduction. Although OmpR‐P is required for acid‐induced expression of ompR in wild‐type cells, OmpR is not needed for ompR transcription in the absence of H‐NS. Thus, the role of OmpR‐P in autoinduction is to help to counteract repression by H‐NS. This evidence, combined with the finding that relaxing DNA supercoiling with novobiocin also increased ompR transcription, suggests that acid stress induces ompR by altering local DNA topology, not by changing the phosphorylation status of OmpR.
Bilateral intra-industry trade flows and intellectual property rights protections: further evidence from the United Kingdom

ABSTRACT This paper investigates the relationship between the United Kingdom's (hereafter referred as UK) bilateral intra-industry trade (IIT) and foreign intellectual property rights (IPRs) protections. The empirical investigation is based on pooled UK data and benefits from the theoretical distinction between horizontal and vertical IIT. It also estimates a gravity equation for international trade using both fixed and random effects models. We then extend the analysis by employing the GMM system for dynamic panel models. The principal findings suggest that the UK's IIT is stimulated when the level of a trading partner's IPRs and its imitative ability are considered jointly. However, when IPRs and imitation abilities are considered separately, their disparate effects are not an important factor in determining UK IIT flows.
The chemical biology of S-nitrosothiols.

SIGNIFICANCE S-nitrosothiol formation and protein S-nitrosation is an important nitric oxide (NO)-dependent signaling paradigm that is relevant to almost all aspects of cell biology, from proliferation, to homeostasis, to programmed cell death. However, the mechanisms by which S-nitrosothiols are formed are still largely unknown, and there are gaps of understanding between the known chemical biology of S-nitrosothiols and their reported functions. RECENT ADVANCES This review attempts to describe the biological chemistry of S-nitrosation and to point out where the challenges lie in matching the known chemical biology of these compounds with their reported functions. The review will detail new discoveries concerning the mechanisms of the formation of S-nitrosothiols in biological systems. CRITICAL ISSUES Although S-nitrosothiols may be formed with some degree of specificity on particular protein thiols, through un-catalyzed chemistry, and mechanisms for their degradation and redistribution are present, these processes are not sufficient to explain the vast array of specific and targeted responses of NO that have been attributed to S-nitrosation. Elements of catalysis have been discovered in the formation, distribution, and metabolism of S-nitrosothiols, but it is less clear whether these represent a specific network for targeted NO-dependent signaling. FUTURE DIRECTIONS Much recent work has uncovered new targets for S-nitrosation through either targeted or proteome-wide approaches There is a need to understand which of these modifications represent concerted and targeted signaling processes and which is an inevitable consequence of living with NO. There is still much to be learned about how NO transduces signals in cells and the role played by protein S-nitrosation.
Big data clone detection using classical detectors: an exploratory study

Big data analysis is an emerging research topic in various domains, and clone detection is no exception. The goal is to create big data inter‐project clone corpora across open‐source or corporate‐source code repositories. Such corpora can be used to study developer behavior and to reduce engineering costs by extracting globally duplicated efforts into new APIs and as a basis for code completion and API usage support. However, building scalable clone detection tools is challenging. It is often impractical to use existing state‐of‐the‐art tools to analyze big data because the memory and execution time required exceed the average user's resources. Some tools have inherent limitations in their data structures and algorithms that prevent the analysis of big data even when extraordinary resources are available. These limitations are impossible to overcome if the source code of the tool is unavailable or if the user lacks the time or expertise to modify the tool without harming its performance or accuracy. In this research, we have investigated the use of our shuffling framework for scaling classical clone detection tools to big data. The framework achieves scalability on commodity hardware by partitioning the input dataset into subsets manageable by the tool and computing resources. A non‐deterministic process is used to randomly ‘shuffle’ the contents of the dataset into a series of subsets. The tool is executed for each subset, and its output for each is merged into a single report. This approach does not require modification to the subject tools, allowing their individual strengths and precision to be captured at an acceptable loss of recall. In our study, we explored the performance and applicability of the framework for the big data dataset, IJaDataset 2.0, which consists of 356 million lines of code from 25,000 open‐source Java projects. We begin with a computationally inexpensive version of our framework based on pure random shuffling. This version was successful at scaling the tools to IJaDataset but required many subsets to achieve a desirable recall. Using our findings, we incrementally improved the framework to achieve a satisfactory recall using fewer resources. We investigated the use of efficient file tracking and file‐similarity heuristics to bias the shuffling algorithm toward subsets of the dataset that contain undetected clone pairs. These changes were successful in improving the recall performance of the framework. Our study shows that the framework is able to achieve up to 90–95% of a tool's native recall using standard hardware. Copyright © 2014 John Wiley & Sons, Ltd.
The importance and pitfalls of correlational science in palliative care research

Purpose of reviewCorrelational science discovers associations between patient characteristics, symptoms and biomarkers. Correlational science using data from cross-sectional studies is the most frequently applied study design in palliative care research. The purpose of this review is to address the importance and potential pitfalls in correlational science. Recent findingsAssociations observed in correlational science studies can be the basis for generating hypotheses that can be tested in experimental studies and are the basic data needed to develop classification systems that can predict patient outcomes. Major pitfalls in correlational science are that associations do not equate with causality and that statistical significance does not necessarily equal a correlation that is of clinical interest. Researchers should be aware of the end-points that are clinically relevant, that end-points should be defined before the start of the analyses, and that studies with several end-points should account for multiplicity. SummaryCorrelational science in palliative care research can identify related clinical factors and biomarkers. Interpretation of identified associations should be done with careful consideration of the limitations underlying correlational analyses.
Further analysis on strange evolution behavior of 7-bit binary string strategies in iterated prisoner's dilemma game

Evolution of cooperation has been actively studied in the evolutionary computation (EC) community mainly for the iterated prisoner's dilemma (IPD) game. One of the frequently examined settings is a noisy environment where a player chooses a different action from the suggested one by its strategy with a pre-specified error probability. The use of the error probability in the IPD game usually makes the evolution of cooperation very difficult. This is because occasional defection by error disturbs mutual cooperation. In our former study, we examined the effect of the error probability on the evolution of cooperation among players with binary string strategies under various settings of memory length. Then we found that a higher average payoff was obtained by increasing the error probability from zero to a small value only when we used 7-bit binary string strategies with a memory about the opponent's previous two actions. That is, a small error probability helped the evolution of cooperation only under this particular setting. This behavior was not observed in the other settings of memory usage. In this paper, we further examine this behavior through computational experiments for a wide variety of settings of various factors. Experimental results show that this behavior is observed only under special settings of the following factors: the number of players (i.e., population size), memory length, memory usage, and a crossover operator.
Role of laminin in the Morphogenetic cascade during Coculture of sertoli cells with peritubular cells

Observations summarized in this article demonstrate an essential role of laminin during the restructuring processes that occur during coculture of Sertoli cells with testicular peritubular cells. The data presented indicate that laminin becomes detectable on the free surfaces of Sertoli cells only after reaggregation of Sertoli cells begins, coincident with the initiation of repolarization at a specific stage of the morphogenetic cascade. We infer that laminin deposited at this time serves as a cohesion molecule that permits peritubular cells to come into close contact with Sertoli cells and subsequently to spread along the free surfaces of Sertoli cells. These conclusions and inferences are based on the following experiments. Cycloheximide‐treated peritubular cells in culture in MEM containing cycloheximide readily attach to laminin‐coated polystyrene surfaces. By contrast, added peritubular cells do not attach onto monolayers of Sertoli cells in monoculture or onto Sertoli cells plated on top of peritubular cells and maintained in coculture for periods of up to 48 h in cocultures maintained for 6 days, however, labeled peritbular cells readily adhere to the free surfaces of reaggregated Sertoli cells. Laminin, but not fibronectin, appears on the free surfaces of the reaggregated Sertoli cells atthis time, coinciding with the period of initial mound formation. The addition of antilaminin IgG, but not antifibronectin IgG, blocks the attachment of cycloheximide‐treated peritubular cells to laminin‐coated plates and also blocks the subsequent migration of peritubular cells required to form a monolayer. Similarly, anti‐laminin IgG inhibits the attachment and spreading of labeled peritubular cells seeded on the free surfaces of reaggregated Sertoli cells in mounds generated during the morphogenetic cascade. We interpret the combined data to indicate that the appearance of laminin on the free surfaces of Sertoli cells is required to permit peritubular cells to adhere and subsequently to migrate on Sertoli cell surfaces, resulting in the formation of a tubule‐like structure. © 1994 Wiley‐Liss, Inc.
Evaluation of a New Machine for Flower and Fruit Thinning in Stone Fruits

Peach and apricot trees usually set more fruit than they can adequately support. Crop load adjustment through fruit thinning is a routine practice adopted by fruit growers to obtain a marketable product. However, hand thinning is an expensive, labor-intense operation. The interest in the mechanization of thinning has increased in the last decades. A new machine, consisting of a tractor-mounted rotor equipped with elastic rods radially inserted on a central axis, has been recently developed to thin both flowers and green fruits in stone fruit crops. In order to test its effectiveness and optimize the operative conditions, trials were carried out in 2016 in two apricot and two peach commercial orchards located in the northeast Italy. Tests were carried out on narrow-canopied orchards, during blooming time, and on green fruit, assessing the flower and fruit removal percentage and the labor saving as compared with the standard fruit hand-thinning practice. In apricot, the machine removed 20.8% of flowers and 43.6% of fruit, allowing 48% time saving in the follow-up fruit manual thinning as compared with the control (hand-thinning only). In peach, mechanical thinning at blooming time removed 63% of flowers, allowing 42.4% time saving in the follow-up fruit manual thinning as compared with the control, whereas mechanical thinning of fruit at the beginning of pit hardening stage removed less than 10%. The development of a mechanical thinning practice, complemented by a manual finishing, could represent a valuable near-term solution to reduce thinning labor time.
Bilateral paramedian thalamic syndrome: abnormal circadian wake-sleep and autonomic functions

Objectives: To describe wake-sleep and body core temperature (t°) rhythm abnormalities in two patients with bilateral paramedian thalamic calcifications. Methods: Patients underwent (18F)FDG PET scans and 24 hour polygraphic recordings of wake-sleep and t°. Results: PET showed bilateral thalamic hypometabolism in both patients with additional basal ganglia or mesiolateral frontal and cingular hypometabolism. Wake-sleep studies showed abnormal sleep organisation and in the case with frontal and limbic PET hypometabolism, pre-sleep behaviour associated with “subwakefulness” EEG activities, lack of EEG spindles and K complexes, and features of status dissociatus. The t° rhythms showed increased mesor in both (37.4°C and 37.75°C) and inverted rhythm in one patient. Conclusions: Paramedian thalamic structures and interconnected, especially frontal and cingular, areas play a part in the organisation of the wake-sleep cycle and attendant autonomic functions.
Enhanced muscle fat oxidation and glucose transport by ACRP30 globular domain: Acetyl–CoA carboxylase inhibition and AMP-activated protein kinase activation

gACRP30, the globular subunit of adipocyte complement-related protein of 30 kDa (ACRP30), improves insulin sensitivity and increases fatty acid oxidation. The mechanism by which gACRP30 exerts these effects is unknown. Here, we examined if gACRP30 activates AMP-activated protein kinase (AMPK), an enzyme that has been shown to increase muscle fatty acid oxidation and insulin sensitivity. Incubation of rat extensor digitorum longus (EDL), a predominantly fast twitch muscle, with gACRP30 (2.5 μg/ml) for 30 min led to 2-fold increases in AMPK activity and phosphorylation of both AMPK on Thr-172 and acetyl CoA carboxylase (ACC) on Ser-79. Accordingly, concentration of malonyl CoA was diminished by 30%. In addition, gACRP30 caused a 1.5-fold increase in 2-deoxyglucose uptake. Similar changes in malonyl CoA and ACC were observed in soleus muscle incubated with gACRP30 (2.5 μg/ml), although no significant changes in AMPK activity or 2-deoxyglucose uptake were detected. When EDL was incubated with full-length hexameric ACRP30 (10 μg/ml), AMPK activity and ACC phosphorylation were not altered. Administration of gACRP30 (75 μg) to C57 BL/6J mice in vivo led to increased AMPK activity and ACC phosphorylation and decreased malonyl CoA concentration in gastrocnemius muscle within 15–30 min. Both in vivo and in vitro, activation of AMPK was the first effect of gACRP30 and was transient, whereas alterations in malonyl CoA and ACC occurred later and were more sustained. Thus, gACRP30 most likely exerts its actions on muscle fatty acid oxidation by inactivating ACC via activation of AMPK and perhaps other signal transduction proteins.
Changes in cardio-ankle vascular index in smoking cessation.

AIM To investigate the effect of smoking and smoking cessation on cardio-ankle vascular index (CAVI). METHODS The subjects were 82 smokers (77 men, 64+/-10 years) and 20 non-smokers (18 men, 61+/-7 years). CAVI was measured every 3 months and CAVI severity was classified into 3 levels. Decreased, unchanged, and increased CAVI severity levels were coded as "improvement," "no change," and "exacerbation," respectively. Smoking status was coded as "success" for complete abstinence, "partial success" for a reduced number of cigarettes, and "failure" for an unchanging number of cigarettes. RESULTS Compared with non-smokers, smokers showed a higher CAVI (p<0.05) prior to smoking cessation. Post-cessation, CAVI improved from 9.4 to 8.6 (p<0.01) in "success" cases (n=22), and the significant pre-cessation difference from non-smokers (n=20, CAVI=8.8) disappeared. With regard to the change in CAVI severity of each smoking status, "improvement" occurred in 17%, 24%, and 68% of "failure" (n=35), "partial success" (n=25), and "success" (n=22) groups, respectively, and the "success" group was significantly higher than the other two groups. CONCLUSION The study showed that CAVI was increased by smoking, and complete smoking cessation improved CAVI.