Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosomal directionality of DNA mismatch repair in Escherichia coli

Significance DNA mismatch repair (MMR) is critical to avoid mutations that can lead to genetic disease, cancer, and death. The MMR system is evolutionarily conserved from bacteria to humans and is an example of a remarkable molecular machine. Here we show that this machine operates unidirectionally with respect to the chromosome of Escherichia coli. The most likely explanation for this directionality is that the MMR machinery is associated with the complex responsible for DNA replication. We suggest that this association facilitates the mechanism of strand discrimination in MMR. Defects in DNA mismatch repair (MMR) result in elevated mutagenesis and in cancer predisposition. This disease burden arises because MMR is required to correct errors made in the copying of DNA. MMR is bidirectional at the level of DNA strand polarity as it operates equally well in the 5′ to 3′ and the 3′ to 5′ directions. However, the directionality of MMR with respect to the chromosome, which comprises parental DNA strands of opposite polarity, has been unknown. Here, we show that MMR in Escherichia coli is unidirectional with respect to the chromosome. Our data demonstrate that, following the recognition of a 3-bp insertion-deletion loop mismatch, the MMR machinery searches for the first hemimethylated GATC site located on its origin-distal side, toward the replication fork, and that resection then proceeds back toward the mismatch and away from the replication fork. This study provides support for a tight coupling between MMR and DNA replication.
A comprehensive survey on safe reinforcement learning

Safe Reinforcement Learning can be defined as the process of learning policies that maximize the expectation of the return in problems in which it is important to ensure reasonable system performance and/or respect safety constraints during the learning and/or deployment processes. We categorize and analyze two approaches of Safe Reinforcement Learning. The first is based on the modification of the optimality criterion, the classic discounted finite/infinite horizon, with a safety factor. The second is based on the modification of the exploration process through the incorporation of external knowledge or the guidance of a risk metric. We use the proposed classification to survey the existing literature, as well as suggesting future directions for Safe Reinforcement Learning.
Is complexity really the enemy of software security?

Software complexity is often hypothesized to be the enemy of software security. We performed statistical analysis on nine code complexity metrics from the JavaScript Engine in the Mozilla application framework to investigate if this hypothesis is true. Our initial results show that the nine complexity measures have weak correlation (ρ=0.30 at best) with security problems for Mozilla JavaScript Engine. The study should be replicated on more products with design and code-level metrics. It may be necessary to create new complexity metrics to embody the type of complexity that leads to security problems.
Optimal Design of E-Commerce Site Infrastructure from a Business Perspective

A methodology for designing data center infrastructure for E-commerce sites is developed. It differs from existing methodologies in that it evaluates and compares alternative designs from a business perspective, that is, by evaluating the business impact (financial loss) imposed by imperfect infrastructure. The methodology provides the optimal infrastructure that minimizes the sum of provisioning costs and business losses incurred during failures and performance degradations. A full numerical example design is provided and results are analyzed. The use of the method for dynamically provisioning an adaptive infrastructure is briefly discussed.
Rules for Dividing a Disputed Resource in the Context of the Classical Liberal Argument for Peace

Abstract In this paper, we study alternative forms of conflict resolution, both peaceful and non-peaceful, between two countries that compete for claims to a resource used to produce potentially traded goods. Consistent with the classical liberal argument, peace supports mutually beneficial trade, whereas war preempts it. War always induces countries to allocate resources into non-contractible arming (“guns”) for superiority in conflict. Under peaceful settlement, countries might choose to arm as well for gaining leverage in negotiations, but arming is typically less than what it is under war. Building on the observation that arming itself affects the countries’ bargaining sets, we compare the efficiency properties of division rules generated by three prominent bargaining solutions – namely, splitting the surplus, equal sacrifice, and Nash bargaining – and show how they depend on the gains from trade.
How Disasters Affect Local Labor Markets: The Effects of Hurricanes in Florida

This study improves upon the Difference in Difference approach by examining exogenous shocks using a Generalized Difference in Difference (GDD) technique that identifies economic effects of hurricanes. Based on the Quarterly Census of Employment and Wages data, worker earnings in Florida counties hit by a hurricane increase up to 4 percent, whereas earnings in neighboring counties decrease. Over time, workers experience faster earnings and slower employment growth than workers in unaffected counties. Hurricanes have a greater impact in coastal and Panhandle counties, and powerful hurricanes have greater economic effects than weaker ones. Further, the GDD technique is applicable to analyze a wider range of exogenous shocks than hurricanes.
Quantitation of human herpes virus 6 genome in children with acute lymphoblastic leukemia

Acute lymphoblastic leukemia is the main type of leukemia in children. An infectious etiology has been suspected and the role of the Human herpesvirus‐6 (HHV‐6) has been suggested. Several studies have tried to establish a link between HHV‐6 infections and hematological malignancies, with discordant results. The potential role of HHV‐6 in the pathogenesis of pediatric acute lymphoblastic leukemia was investigated. HHV‐6 genome copy number was measured by quantitative real‐time PCR (RQ‐PCR) in bone marrow or peripheral blood samples obtained from 36 children (median age = 4 years) with B acute lymphoblastic leukemia (n = 31) and T acute lymphoblastic leukemia (n = 5) at diagnosis and during complete remission. Positive samples were further characterized to define viral variant, A or B. A total of 24.7% of samples were positive for HHV‐6 genome: 13.9% were leukemia samples and 34.1% were complete remission samples. Viral load was low with values lower at diagnosis (median viral copy number = 22.9) than at complete remission (median copy number = 60.1). Among the 17 patients with positive samples, 15 were typed as B‐variant whereas 2 could not be typed. These results argue against a role of HHV6 infection in the development of pediatric acute lymphoblastic leukemia. They also suggest that HHV‐6 may infect latently bone marrow progenitors but seems not able to infect leukemic cells, raising again the question of the mechanism of virus fusion and entry. This observation shows that a reactivation may be observed during complete remission supporting the possibility of virus reactivation in immunocompromised hosts. J. Med. Virol. 80:689–693, 2008. © 2008 Wiley‐Liss, Inc.
The Origins of AIDS

reality, often means ‘‘establish’’) basic primary health-care services that deal with the full gamut of health issues than spend huge sums to eradicate a single disease, but she does not delve into the difficulties and costs this entails. Model pilot programs often appear to be successful, while the reality, in the poor, rural countryside, is all too frequently poorly trained and supervised health workers who are only occasionally at their posts, with little in the way of vital drugs and equipment. Focused eradication programs, generally vertical in nature, have the advantage of focusing a government’s commitment and subjecting it to international scrutiny and accountability.
Executive Stress

I HOPE that the first point I want to make about executive stress has also been made, equally emphatically. by my colleagues who are also contributing to this issue. It is, of course, that "executive stress" is no different from maternal stress, geriatric stress, boilermakers' stress, and so on. Because we live in an age of classification we are happy when we can tie a label on to something and, having done this and filed it away, we tend to think that we can happily leave it there. Stress is now a fashionable word, and we have convinced ourselves that we are, all of us, living in stressful times. Maybe we are, but this does not absolve us from the responsibility of doing something about it. Some stress essential It tends to be forgotten that a reasonable amount of stress, or challenge. is not only good for us, but virtually essential to keep us toned up and ticking over actively. Problems start when the degree of stress becomes too much for the individual.
Pharmacokinetics of oral vitamin C

Purpose . To test whether plasma vitamin C levels, following oral doses in supplemented volunteers, are tightly controlled and subject to a maximum in the region of 220 mML 21 , as suggested by previous researchers for depleted subjects. To determine plasma levels following single, variable-sized doses of standard and liposomal formulations of vitamin C and compare the effects of the different formulations. To determine whether plasma levels above ,280 mML 21 , which have selectively killed cancer, bacteria or viruses (in laboratory experiments), can be achieved using oral doses of vitamin C. Design . This was a single blind study, measuring plasma levels in two subjects, in samples taken halfhourly or hourly for 6 hours, following ingestion of vitamin C. Data were compared with published results and with data from 10 years of laboratory plasma determinations. Materials and methods . Standard 1 gram tablets of vitamin C; liposomal vitamin C. Plasma levels were analysed using the method of Butts and Mulvihill. Results . Preliminary investigations of the effects of liposomal and standard formulation ascorbate showed that blood plasma levels in excess of the previously assumed maximum of 220 mML 21 are possible. Large oral doses of liposomal ascorbate resulted in plasma levels above 400 mML 21 . Conclusions . Since a single oral dose can produce plasma levels in excess of 400 mML 21 , pharmacokinetic theory suggests that repeated doses could sustain levels well above the formerly assumed maximum. These results have implications for the use of ascorbate, as a nutrient and as a drug. For example, a short in vitro treatment of human Burkitt’s lymphoma cells with ascorbate, at 400 mML 21 , has been shown to result in ,50% cancer cell death. Using frequent oral doses, an equivalent plasma level could be sustained indefinitely. Thus, oral vitamin C has potential for use as a non-toxic, sustainable, therapeutic agent. Further research into the experimental and therapeutic aspects of high, frequent, oral doses of ascorbic acid either alone or (for cancer therapy) in combination with synergistic substances, such as alpha-lipoic acid, copper or vitamin K3, is needed urgently.
Evolutionary Cognitive Psychology

Traditional cognitive psychology, the study of the information processing mechanisms underlying human thought and behavior, is problematic from an evolutionary viewpoint: Humans were not directly selected to process information, nor to store it, learn it, attend to it, represent it—nor even, in fact, to think. All of these capacities, the core topics of cognitive psychology, can be seen as epiphenomena arising over the course of evolution from the need to get the central jobs done: survival and reproduction. Moreover, while the subtasks of those two main goals—finding food, maintaining body temperature, selecting a mate, negotiating status hierarchies, forming cooperative alliances, fending off predators and conspecific competitors, raising offspring, etc.—surely relied on gathering and processing information, meeting the challenges of each of these domains would only have been possible by in each case gathering specific pieces of information and processing it in particular ways. This suggests that to best study the faculties of memory, or attention, or reasoning, we should take a taskand domain-specific approach that focuses on the use of each faculty for a particular evolved function, just the approach exemplified by the other chapters in this handbook.
> Replace This Line with Your Paper Identification Number (double-click Here to Edit) < 1

—This paper describes a CMOS vision sensor which is inspired by biological visual systems. Each pixel independently and in continuous time quantizes local relative intensity changes to generate spike events. These events appear at the output of the sensor as an asynchronous stream of digital pixel addresses. These address-events signify scene reflectance change and have sub-millisecond timing precision. The output data rate depends on the dynamic content of the scene and is typically orders of magnitude lower than those of conventional frame-based imagers. By combining an active front-end logarithmic photoreceptor running in continuous time with a self-timed switched-capacitor differencing circuit, the sensor achieves an array mismatch of 2.1% in relative intensity event threshold and a pixel bandwidth of 3 kHz under 1 klux scene illumination. Dynamic range is >120 dB and chip power consumption is 23 mW. Event latency shows weak light dependency and decreases to 15 us at >1 klux pixel illumination. The sensor is built in a 0.35u 4M2P process yielding 40x40 um 2 pixels with 9.4% fill-factor. By providing high pixel bandwidth, wide dynamic range, and precisely-timed sparse digital output, this neuromorphic silicon retina provides an attractive combination of characteristics for low-latency dynamic vision under uncontrolled illumination with low post-processing requirements.
MicroRNA in Breast Cancer — Gene Regulators and Targets for Novel Therapies

MicroRNAs (miRNAs) are a recently discovered class of endogenously expressed, single stranded, non-protein coding RNAs of about 19-25 nucleotides in length, that bind to the 3` un-translated regions (UTR) of target messenger RNAs (mRNAs) through complementarity with the first 2-8 nucleotides at the 5` end of the miRNA. They play important roles in diverse biological and pathological processes, through the regulation of gene expression at both transcriptional and post-transcriptional level [1,2]. The miRNA-mediated gene regulation is part of a larger mechanism known as RNA interference which involves other regulatory RNAs; small interfering RNAs (siRNA), which induce silencing of specific mRNA through comple‐ mentary nucleotide sequences, and piwi-interfering RNAs (piRNAs) which, through similar mechanisms, induce silencing of active mobile elements to maintain germ line integrity and fertility. To date, over 1000 miRNAs and 16,228,619 predicted mRNA target sites have been identified, affecting over 30% of the human genome [3]. What makes them important players in regulating protein expression is the ability of a single miRNA to interact with more than one target gene (due to the imperfect matching between miRNA and its target which still produces a functional effect). In addition, a single gene can be regulated by multiple miRNAs. Currently, around 200 human transcription factor-miRNA relationships have been described and collated into the TransmiR database [4]. These include transcription factors such as Nanog and Oct3/4, [5], hormones such as estradiol [6], and tumor suppressor genes such as p53 [7]. Since the initial reports of the miRNAs lin-4 and let-7 as developmental regulators of Caeno‐ rhabditis elegans (C. elegans) [8,9], there have been numerous studies describing the involvement of miRNAs in normal cellular function as well as in various disease conditions, such as cardiac arrhythmias [10,11], fibrosis [12,13], remodeling [14,15], metabolic disorders [16], diabetes [17],
Comparison of Midazolam and Propofol for Sedation in Pediatric Diagnostic Imaging Studies

Abstract Objective: This study aims to compare the efficacy of propofol and midazolam in terms of adverse effect potentials and to determine the appropriate strategy for pediatric procedural sedation. Methods: A total of 200 pediatric patients (aged < 14 years) undergoing diagnostic procedures were recruited for this nonrandomized prospective controlled cohort study. The patients were assigned to 2 treatment arms: either propofol (Group 1: IV bolus dose of 2 mg/kg during a 2-minute period, IV maintenance dose of 100 mcg/kg/min) or midazolam (Group 2: IV bolus dose of 0.15 mg/kg during a period of 2 to 3 minutes) to achieve sedation. Demographic data, body weight, and clinical status of the patients were evaluated and recorded. The vital signs and sedation levels (ie, Ramsay sedation scale scores) were evaluated and recorded, as well as the complications detected and medications administered in 10-minute intervals throughout the sedation procedure. Findings between the study arms were compared. Results: Arterial blood pressures decreased significantly in both groups (P = 0.001). The patients in Group 1 experienced a greater difference in diastolic blood pressure (P = 0.001) than those in Group 2. Sedation scores in Group 1 were more favorable (P = 0.014) and reached the appropriate sedation level in a shorter time than those in Group 2 (P = 0.010). Likewise, recovery time of patients was shorter in Group 1 than in Group 2 (P = 0.010). Hypoxia was found to be more common in the propofol group, but the difference was not significant (P = 0.333). Conclusion: Propofol seems to be more effective, achieve the appropriate sedation level more quickly, and provide a faster onset of sedation than midazolam in pediatric procedural sedation and analgesia. Propofol is preferred for imaging studies (computed tomography and magnetic resonance imaging) to reduce the occurrence of undesired motion artefacts. Although both drugs are safe to use for sedation before pediatric imaging procedures, propofol is preferred with appropriate preparation.
Software defect prediction based on geometric mean for subspace learning

Due to the confusion of fault-prone software modules and non-fault-prone ones, and the limit of traditional mothed such as LDA and PCA, the performance of software defect prediction model is difficult to improve. In this paper, we present GMCRF, a method based on dimensionality reduction technique and conditional random field (CRF) for software defect prediction. In our proposed method, firstly, we leverage geometric mean for subspace learning to choose the best combination of features from data set. Secondly, we propose to apply the best combination of features which is selected by geometric mean-based approach in CRF model. Interestingly, we find that the GMCRF method achieves much better final results than the other approach as shown in the software defect data classification task.
Modulation of Memory Formation by Stimulus Content: Specific Role of the Medial Prefrontal Cortex in the Successful Encoding of Social Pictures

It is unclear whether the involvement of the medial prefrontal cortex (mPFC) during encoding is restricted to the evaluative processing of to-be-encoded stimuli or if it is instead actively engaged during memory formation. The difficulty of assessing the contribution of the mPFC to encoding based on previous neuroimaging studies partly arises from the use of several types of stimuli, such as emotional or social ones. These different types of stimulus content could differently modulate mPFC activity during memory formation and thus partly explain the variable contribution of this region to encoding. Using emotional/neutral and social/nonsocial pictures, we conducted an event-related functional magnetic resonance imaging study using a subsequent memory paradigm as the main analytical strategy. We observed that the brain activity in the dorsal and orbital mPFC is significantly and specifically predictive of the successful encoding of social compared with nonsocial pictures. In contrast, the activity in the amygdala specifically predicts the successful encoding of emotional compared with neutral pictures. The modulation of the mPFC by social information in a memory encoding context could be associated with the initiation of self-referential processes whose contribution is to enhance memory formation.
Statistical analysis of the mechanical properties of natural fibers and their composite materials. I. Natural fibers

In this study, we extended a statistical approach to develop a comparative study on the behavior of different natural fibers such as flax, jute, abaca, and sisal. In particular, the dimensional characterization and mechanical properties of natural fibers were considered. The wide dispersion of fiber properties, which is a well-known characteristic of natural systems, has been described here by means of a new advanced statistical approach based on neural network algorithms that can provide a more accurate prediction of the behavior of natural fibers. The new statistical model was developed to interpolate the experimental data, using algorithms based on neural networks. POLYM. COMPOS. , 2008. © 2008 Society of Plastics Engineers
Antipsychotic medication adherence and satisfaction among Palestinian people with schizophrenia.

BACKGROUND In Arab and Muslim-dominated countries, spirituality and religiosity shape the belief and practices toward chronic illnesses. No previous studies were published to assess adherence to and satisfaction with antipsychotic medications in persons with schizophrenia in the Arab world. OBJECTIVE To assess medication adherence and treatment satisfaction with antipsychotics in a sample of Palestinian people with schizophrenia. METHODOLOGY Medication adherence was assessed using the 8-item Morisky Medication Adherence Scale (MMAS-8). Treatment satisfaction was assessed using the Treatment Satisfaction Questionnaire for Medication (TSQM 1.4). Psychiatric symptoms were assessed using the expanded Brief Psychiatric Rating Scale (BPRS-E). Data were entered and statistically analyzed using SPSS 16 for windows. RESULTS A convenience sample of 131 persons with schizophrenia was studied. Based on MMAS-8, 44 persons (33.6%) had a low rate, 58 (44.3%) had a medium rate and 29 (22.1%) had a high rate of adherence. Age was significantly correlated (P=0.028) with adherence score. However, variables like use of monotherapy or atypical or depot antipsychotics were not significantly associated with higher adherence. The means of satisfaction with regard to effectiveness, side effects, convenience and global satisfaction were 72.6 ± 20.5, 67.9 ± 31.47, 63.2 ± 14.3 and 63.1 ± 18.8 respectively. There was a significant difference in the means of effectiveness (P < 0.01), convenience (P < 0.01), global satisfaction (P < 0.01), but not side effects domains (P=0.1) among persons with different levels of adherence. Furthermore, there was a significant difference in the means of positive symptom score (P < 0.01), manic (P < 0.01) and depression (P < 0.01) but not negative symptom score (P=0.4) among persons with different levels of adherence. CONCLUSIONS Medication nonadherence was common and was associated with low treatment satisfaction scores and poor psychiatric scores. Medication related factors had insignificant effects on adherence scores.