Miracle-dz/UniFAR-FTUs huggingface dataset:
Alterations in Cerebral Mitochondria during Acute Hypoglycemia

To test the hypothesis that acute hypoglycemia leads to free radical induced alterations in cerebral mitochondria, newborn piglets were subjected to 2 h of insulin-induced hypoglycemia (blood glucose 1 mmol/l). The effects of free radicals were determined in cerebral cortical synaptosomes, mitochondria, and neuronal nuclei by measuring membrane lipid peroxidation. Fragmentation of nuclear and mitochondrial DNA was also examined. Lipid peroxidation was significantly increased in hypoglycemic mitochondrial membranes as compared to controls, but no increase in peroxidation in hypoglycemic synaptosomal or nuclear membranes was observed. An increase in low molecular weight DNA fragments was observed only in mitochondrial DNA from hypoglycemic piglets. We speculate that alteration of cerebral mitochondria due to increased free radical production is one of the early events in the pathogenesis of hypoglycemic brain injury.
Divergence of the diapause transcriptome in apple maggot flies: winter regulation and post-winter transcriptional repression

ABSTRACT The duration of dormancy regulates seasonal timing in many organisms and may be modulated by day length and temperature. Though photoperiodic modulation has been well studied, temperature modulation of dormancy has received less attention. Here, we leverage genetic variation in diapause in the apple maggot fly, Rhagoletis pomonella, to test whether gene expression during winter or following spring warming regulates diapause duration. We used RNAseq to compare transcript abundance during and after simulated winter between an apple-infesting population and a hawthorn-infesting population where the apple population ends pupal diapause earlier than the hawthorn-infesting population. Marked differences in transcription between the two populations during winter suggests that the ‘early’ apple population is developmentally advanced compared with the ‘late’ hawthorn population prior to spring warming, with transcripts participating in growth and developmental processes relatively up-regulated in apple pupae during the winter cold period. Thus, regulatory differences during winter ultimately drive phenological differences that manifest themselves in the following summer. Expression and polymorphism analysis identify candidate genes in the Wnt and insulin signaling pathways that contribute to population differences in seasonality. Both populations remained in diapause and displayed a pattern of up- and then down-regulation (or vice versa) of growth-related transcripts following warming, consistent with transcriptional repression. The ability to repress growth stimulated by permissive temperatures is likely critical to avoid mismatched phenology and excessive metabolic demand. Compared with diapause studies in other insects, our results suggest some overlap in candidate genes/pathways, though the timing and direction of changes in transcription are likely species specific. Summary: Transcriptomics reveals that summer emergence timing of flies is regulated during winter, while initial transcriptional responses to post-winter warming are largely suppressed.
Nature, Nurture, and Human Behavior; an Endless Debate

This editorial aims at addressing the endless debate concerned with the extent to which particular aspects of behavior are a product of either nature ( inherited i.e. genetic), nurture (acquired i.e. learned), or their interaction. In spite of the philosophical conflict between nativists who adopt an extreme hereditary position i.e. attributing everything to biological factors (nature) and environmentalists who believe that the way we are brought up (nurture) totally governs the psychological aspects of our childhood development through learning, it is hardly today to accept either of these extreme positions. There are simply too many “facts” on both sides of the argument which are inconsistent with an “all or none” view. So instead of asking whether the child development is down to nature or nurture, the question has been reformulated to “How much? ” i.e., considering the fact that both heredity and environment influence the person we become, which is the more important? This is really the individualized question that needs to be answered. Lastly but by no means least, sorting out what is the cause and what is the effect is no mere academic matter. If we are really trying to help people’s lives, it is essential to get it right.
Effect of improved management practices on economics in Groundnut (Arachis hypogaea L.) cultivation

An experiment was carried out during kharif season of 2016 at Hiregundgal District: Tumkur (Karnataka) at five location under the project of Bhoo Samruddhi collaboration between KSDA (Karnataka State Department of Agriculture) and ICRISAT (International Crop Research Institute for Semi-Arid Tropics Agriculture). To study the “Effect of improved management practices on factor of productivity on Groundnut (Arachis hypogaea L.) cultivation” Economic viability of groundnut proved superior in recommended dose of fertilizer (25:50:25 NPK+ Gypsum @ 500 kg ha-1) along with micro nutrient (ZnSO4@ 25 kg ha-1& Borax @ 10 kg ha-1) than recommended dose of fertilizer. Broad bed and furrow was superior over flat bed. Cultivated variety ICGV 91114 superior to cultivated variety K 6. Farmer’s practice registered the lowest value for economics compared to all treatments.
Soil gas radon measurements for investigating the actual status of seismic quiescence along the bounding fault of the Ghab pull-apart basin in western Syria

El propósito de este trabajo consistió en investigar posibles cambios de radón relacionados con la zona de falla que pudieran mostrar alguna relación con la tectónica local a lo largo de la zona de falla de la cuenca de Ghab. A pesar de su actividad histórica, la falla de Ghab presenta actualmente una falta de actividad sísmica con un periodo largo de quietud sísmica. Se escogieron 7 sitios para realizar muestreos de radón utilizando un equipo ALPHAGUARD. El valor promedio normal de radón de fondo se obtuvo con medidas realizadas lejos de la zona de influencia de la falla. Se definió un rango estadístico de variaciones anómalas de radón con límites marcados por el valor promedio mas/menos dos desviaciones estándar (X+/- 2DS). Los resultados iniciales muestran incrementos de radón en las estaciones de monitoreo a lo largo de la zona de falla con picos 4-5 veces mayores que el nivel de fondo. Aunque estas concentraciones anómalas relativamente grandes podrían confirmar la utilidad del radón como un posible indicador para trazar los límites de la falla, no prueban necesariamente una relación con la actividad tectónica del área. Sin embargo, estos incrementos de radón podrían indicar una evidencia de zonas con mayor permeabilidad asociadas a la deformación de la estructura en la zona de ruptura.
A Language for Bidirectional Updating Based on Injective Mapping

With the popularity of XML, bidirectional updating – maintaining the consistency between two pieces of structured data, again becomes a problem of interest. In this paper we propose a new framework, inspired by program inversion, to look at this problem. We design a functional language, Inv, in which all programs are injective and their inverses can be trivially constructed. The language is equivalent to reversible Turing machines and expressive enough to describe most transforms one would need. It is assumed that the data to be synchronised are related by a transform written in Inv. The semantics of Inv is then extended to deal with bidirectional updating. Given a transform, its synchronisation behaviour can be derived by algebraic reasoning. The main feature of our approach is being able to deal with duplication and structural changes.
Personality Profiles of Software Engineers and Their Software Quality Preferences

Studies related to human aspects in software engineering (SE) have been performed from different perspectives. These perspectives include the study of human factors in different phases of software life cycle, effect of team performance in software development, how can a personality trait suit a particular task, and about some other miscellaneous issues. This research work aims to establish personality profiles of Pakistani software engineers using the Myers-Briggs Type Indicator (MBTI) instrument. This survey has collected personality profiles of 110 software engineers. Moreover, their preferences of software quality attributes have also been collected. Analysis of the study shows that the most prominent personality type is a combination of introversion, sensing, thinking and judging. Investigative results indicate that most of the software engineers consider usability and functionality as the most important software quality attributes.
Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution

It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons (“exon-intron marking”), linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing.
Database Cracking

Database indices provide a non-discriminative navigational infrastructure to localize tuples of interest. Their maintenance cost is taken during database updates. In this paper, we study the complementary approach, addressing index maintenance as part of query processing using continuous physical reorganization, i.e., cracking the database into manageable pieces. The motivation is that by automatically organizing data the way users request it, we can achieve fast access and the much desired self-organized behavior. We present the ﬁrst mature cracking architecture and report on our implementation of cracking in the context of a full ﬂedged relational system. It led to a minor enhancement to its relational algebra kernel, such that cracking could be piggy-backed without incurring too much processing overhead. Furthermore, we illustrate the ripple eﬀect of dynamic reorganization on the query plans derived by the SQL optimizer. The experiences and results obtained are indicative of a signiﬁcant reduction in system complexity. We show that the resulting system is able to self-organize based on incoming requests with clear performance beneﬁts. This behavior is visible even when the user focus is randomly shifting to diﬀerent parts of the data.
Immunocytochemical Localization of a-Protein Kinase C in Rat Pancreatic/ -Cells during Glucose-induced Insulin Secretion

To investigate the role of protein kinase C (PKC) in the regulation of insulin secretion, we visualized changes in the intracellular localization of tx-PKC in fixed B-cells from both isolated rat pancreatic islets and the pancreas of awake unstressed rats during glucose-induced insulin secretion. Isolated, perifused rat islets were fixed in 4 % paraformaldehyde, detergent permeabilized, and labeled with a mAb specific for ot-PKC. The labeling was visualized by confocal immunofluorescent microscopy. In isolated rat pancreatic islets perifused with 2.75 mM glucose, ot-PKC immunostaining was primarily cytoplasmic in distribution throughout the/3-cells. In islets stimulated with 20 mM glucose, there was a significant redistribution of ot-PKC to the cell periphery. This glucoseinduced redistribution was abolished when either mannoheptulose, an inhibitor of glucose metabolism, or nitrendipine, an inhibitor of calcium influx, were added to the perifusate. We also examined changes in the intracellular distribution of ot-PKC in the/S-cells of awake, unstressed rats that were given an intravenous infusion of glucose. Immunocytochemical analysis of pancreatic sections from these rats demonstrated a glucose-induced translocation of ot-PKC to the cell periphery of the B-cells. These results demonstrate that the metabolism of glucose can induce the redistribution of ot-PKC to the cell periphery of/3-cells, both in isolated islets and in the intact animal, and suggest that tx-PKC plays a role in mediating glucose-induced
Multiclass multiple kernel learning

In many applications it is desirable to learn from several kernels. "Multiple kernel learning" (MKL) allows the practitioner to optimize over linear combinations of kernels. By enforcing sparse coefficients, it also generalizes feature selection to kernel selection. We propose MKL for joint feature maps. This provides a convenient and principled way for MKL with multiclass problems. In addition, we can exploit the joint feature map to learn kernels on output spaces. We show the equivalence of several different primal formulations including different regularizers. We present several optimization methods, and compare a convex quadratically constrained quadratic program (QCQP) and two semi-infinite linear programs (SILPs) on toy data, showing that the SILPs are faster than the QCQP. We then demonstrate the utility of our method by applying the SILP to three real world datasets.
Comparative Analysis of Methods for Identifying Recurrent Copy Number Alterations in Cancer

Recurrent copy number alterations (CNAs) play an important role in cancer genesis. While a number of computational methods have been proposed for identifying such CNAs, their relative merits remain largely unknown in practice since very few efforts have been focused on comparative analysis of the methods. To facilitate studies of recurrent CNA identification in cancer genome, it is imperative to conduct a comprehensive comparison of performance and limitations among existing methods. In this paper, six representative methods proposed in the latest six years are compared. These include one-stage and two-stage approaches, working with raw intensity ratio data and discretized data respectively. They are based on various techniques such as kernel regression, correlation matrix diagonal segmentation, semi-parametric permutation and cyclic permutation schemes. We explore multiple criteria including type I error rate, detection power, Receiver Operating Characteristics (ROC) curve and the area under curve (AUC), and computational complexity, to evaluate performance of the methods under multiple simulation scenarios. We also characterize their abilities on applications to two real datasets obtained from cancers with lung adenocarcinoma and glioblastoma. This comparison study reveals general characteristics of the existing methods for identifying recurrent CNAs, and further provides new insights into their strengths and weaknesses. It is believed helpful to accelerate the development of novel and improved methods.
kR^X: Comprehensive Kernel Protection against Just-In-Time Code Reuse

The abundance of memory corruption and disclosure vulnerabilities in kernel code necessitates the deployment of hardening techniques to prevent privilege escalation attacks. As more strict memory isolation mechanisms between the kernel and user space, like Intel's SMEP, become commonplace, attackers increasingly rely on code reuse techniques to exploit kernel vulnerabilities. Contrary to similar attacks in more restrictive settings, such as web browsers, in kernel exploitation, non-privileged local adversaries have great flexibility in abusing memory disclosure vulnerabilities to dynamically discover, or infer, the location of certain code snippets and construct code-reuse payloads. Recent studies have shown that the coupling of code diversification with the enforcement of a "read XOR execute" (R^X) memory safety policy is an effective defense against the exploitation of userland software, but so far this approach has not been applied for the protection of the kernel itself. In this paper, we fill this gap by presenting kR^X: a kernel hardening scheme based on execute-only memory and code diversification. We study a previously unexplored point in the design space, where a hypervisor or a super-privileged component is not required. Implemented mostly as a set of GCC plugins, kR^X is readily applicable to the x86-64 Linux kernel and can benefit from hardware support (e.g., MPX on modern Intel CPUs) to optimize performance. In full protection mode, kR^X incurs a low runtime overhead of 4.04%, which drops to 2.32% when MPX is available.
What Predicts Online Health Information-Seeking Behavior Among Egyptian Adults? A Cross-Sectional Study

Background Over the last decade, the Internet has become an important source of health-related information for a wide range of users worldwide. Yet, little is known about the personal characteristics of Egyptian Internet users who search for online health information (OHI). Objective The aim of the study was to identify the personal characteristics of Egyptian OHI seekers and to determine any associations between their personal characteristics and their health information-seeking behavior. Methods This cross-sectional questionnaire study was conducted from June to October 2015. A Web-based questionnaire was sent to Egyptian users aged 18 years and older (N=1400) of a popular Arabic-language health information website. The questionnaire included (1) demographic characteristics; (2) self-reported general health status; and (3) OHI-seeking behavior that included frequency of use, different topics sought, and self-reported impact of obtained OHI on health behaviors. Data were analyzed using descriptive statistics and multiple regression analysis. Results A total of 490 participants completed the electronic questionnaire with a response rate equivalent to 35.0% (490/1400). Regarding personal characteristics, 57.1% (280/490) of participants were females, 63.4% (311/490) had a university level qualification, and 37.1% (182/490) had a chronic health problem. The most commonly sought OHI by the participants was nutrition-related. Results of the multiple regression analysis showed that 31.0% of the variance in frequency of seeking OHI among Egyptian adults can be predicted by personal characteristics. Participants who sought OHI more frequently were likely to be female, of younger age, had higher education levels, and good self-reported general health. Conclusions Our results provide insights into personal characteristics and OHI-seeking behaviors of Egyptian OHI users. This will contribute to better recognize their needs, highlight ways to increase the availability of appropriate OHI, and may lead to the provision of tools allowing Egyptian OHI users to navigate to the highest-quality health information.
The CKLF1‐C19 peptide attenuates allergic lung inflammation by inhibiting CCR3‐ and CCR4‐mediated chemotaxis in a mouse model of asthma

To cite this article: Tian L, Li W, Wang J, Zhang Y, Zheng Y, Qi H, Guo X, Zhang Y, Ma D, Shen H, Wang Y. The CKLF1‐C19 peptide attenuates allergic lung inflammation by inhibiting CCR3‐ and CCR4‐mediated chemotaxis in a mouse model of asthma. Allergy 2011; 66: 287–297.
Training in and Experience with Endobronchial Ultrasound

Background: Diagnosing mediastinal and hilar lymphadenopathy and staging lung cancer with endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration (TBNA) are on the rise, but uncertainty surrounds the optimal number of cases needed to achieve acceptable yields. Objectives: To determine the threshold at which EBUS-TBNA reaches adequate yields among trainees and skilled bronchoscopists. Methods: We reviewed all EBUS-TBNAs performed at our medical center since implementing the use of EBUS (n = 222). Results: EBUS-TBNAs were performed in 222 patients (344 nodes). The percentage of adequate specimens sampled (diagnostic specimens or nodal tissue) rose from 66% in 2008 to 90% in 2012 (p < 0.01) and cancer yield improved from 34% in 2008 to 48% in 2012 (p < 0.01). Attending physicians who performed an average of more than 10 procedures per year had higher yields compared to those who performed fewer than 10 procedures per year (86 vs. 68%, p < 0.01). The yield of trainees also improved with every 10 procedures (79, 90 and 95%, p < 0.001) and that of attending physicians with experience (1-25 procedures: 78% yield, 26-50 procedures: 87% yield and 50+ procedures: 90% yield; p < 0.01). Among trainees, failure rates declined steadily. Conclusion: EBUS-TBNA yield (malignant and benign) increases with increasing experience amongst experienced bronchoscopists and trainees as early as the first 20-25 procedures. Pulmonary trainees had a rapid decline in failure rates. These findings suggest that in an academic environment a minimum of 20-25 procedures is needed to achieve acceptable yields.