Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Campylobacter jejuni genes involved in commensal colonization of the chick gastrointestinal tract

Campylobacter jejuni is the leading cause of bacterial gastroenteritis in humans in developed countries throughout the world. This bacterium frequently promotes a commensal lifestyle in the gastrointestinal tracts of many animals including birds and consumption or handling of poultry meats is a prevalent source of C. jejuni for infection in humans. To understand how the bacterium promotes commensalism, we used signature‐tagged transposon mutagenesis and identified 29 mutants representing 22 different genes of C. jejuni strain 81–176 involved in colonization of the chick gastrointestinal tract. Among the determinants identified were two adjacent genes, one encoding a methyl‐accepting chemotaxis protein (MCP), presumably required for proper chemotaxis to a specific environmental component, and another gene encoding a putative cytochrome c peroxidase that may function to reduce periplasmic hydrogen peroxide stress during in vivo growth. Deletion of either gene resulted in attenuation for growth throughout the gastrointestinal tract. Further examination of 10 other putative MCPs or MCP‐domain containing proteins of C. jejuni revealed one other required for wild‐type levels of caecal colonization. This study represents one of the first genetic screens focusing on the bacterial requirements necessary for promoting commensalism in a vertebrate host.
Distribution sort with randomized cycling

Parallel independent disks can enhance the performance of external memory (EM) algorithms, but the programming task is often difficult. Each disk can service only one read or write request at a time; the challenge is to keep the disks as busy as possible. In this article, we develop a randomized allocation discipline for parallel independent disks, called randomized cycling. We show how it can be used as the basis for an efficient distribution sort algorithm, which we call randomized cycling distribution sort (RCD). We prove that the expected I/O complexity of RCD is optimal. The analysis uses a novel reduction to a scenario with significantly fewer probabilistic interdependencies. We demonstrate RCD's practicality by experimental simulations. Using the randomized cycling discipline, algorithms developed for the unrealistic multihead disk model can be simulated on the realistic parallel disk model for the class of multipass algorithms, which make a complete pass through their data before accessing any element a second time. In particular, algorithms based upon the well-known distribution and merge paradigms of EM computation can be optimally extended from a single disk to parallel disks.
Primary Care Physicians' Selection of Low-Intensity Treatments for Patients With Depression.

BACKGROUND AND OBJECTIVES Most outpatient treatment for depression is delivered by primary care physicians (PCPs), yet little is known about which patient variables affect PCPs' selection of high-intensity interventions, namely antidepressant medications or psychotherapy, as opposed to less-intensive treatment regimens (eg, watchful waiting, exercise). Our objective was to ascertain whether the patient's symptom severity, presenting psychosocial stress, and lifestyle habits influenced treatment recommendations. METHODS Forty-two PCPs from six Northeastern US primary care practices provided recommendations in response to vignettes depicting patients with major depressive disorder who varied in symptom severity, psychosocial stressors, and lifestyle habits. RESULTS Low-intensity-only interventions were recommended less than 25% of the time. Lower symptom severity and higher psychosocial stressors were associated with a greater likelihood of "low-intensity interventions only" recommendations. Less-intensive treatments were rarely recommended without more intensive treatments when the vignettes featured severe depression, whereas they were recommended 39% of the time with vignettes featuring mild/moderate symptoms. In response to the mild/moderate vignettes, the presence of psychosocial stressors led to a decreased likelihood of low-intensity-only recommendations. CONCLUSIONS Although vignettes depicting depressed patients with mild/moderate symptoms were more likely to elicit low-intensity treatment recommendations, the frequency was still low. Given the evidence that antidepressants and psychotherapy for mild/moderate depression may be no more effective, and likely less cost-effective, than low-intensity treatments, the findings suggest a need to disseminate knowledge of less intensive treatment options to primary care physicians.
A gene essential for hydrotropism in roots

Roots display hydrotropism in response to moisture gradients, which is thought to be important for controlling their growth orientation, obtaining water, and establishing their stand in the terrestrial environment. However, the molecular mechanism underlying hydrotropism remains unknown. Here, we report that roots of the Arabidopsis mutant mizu-kussei1 (miz1), which are impaired in hydrotropism, show normal gravitropism and elongation growth. The roots of miz1 plants showed reduced phototropism and a modified wavy growth response. There were no distinct differences in morphological features and root structure between miz1 and wild-type plants. These results suggest that the pathway inducing hydrotropism is independent of the pathways used in other tropic responses. The phenotype results from a single recessive mutation in MIZ1, which encodes a protein containing a domain (the MIZ domain) that is highly conserved among terrestrial plants such as rice and moss. The MIZ domain was not found in known genomes of organisms such as green algae, red algae, cyanobacteria, or animals. We hypothesize that MIZ1 has evolved to play an important role in adaptation to terrestrial life because hydrotropism could contribute to drought avoidance in higher plants. In addition, a pMIZ1::GUS fusion gene was expressed strongly in columella cells of the root cap but not in the elongation zone, suggesting that MIZ1 functions in the early phase of the hydrotropic response.
Left and right ventriculo-arterial coupling in a patient with congenitally corrected transposition

The single beat method was used to evaluate right and left ventriculo-arterial coupling in an asymptomatic patient with congenitally corrected transposition. The ratio of ventricular end-systolic to arterial elastances was normal for the left ventricle coupled to the pulmonary circulation, and depressed for the right ventricle coupled to the systemic circulation. This result suggests that chronic uncoupling of the right ventricle to the systemic circulation might play a role in the pathophysiology produced by congenitally corrected transposition.
Caffeine alleviates progressive motor deficits in a transgenic mouse model of spinocerebellar ataxia

Machado–Joseph disease (MJD) is a neurodegenerative spinocerebellar ataxia (SCA) associated with an expanded polyglutamine tract within ataxin‐3 for which there is currently no available therapy. We previously showed that caffeine, a nonselective adenosine receptor antagonist, delays the appearance of striatal damage resulting from expression of full‐length mutant ataxin‐3. Here we investigated the ability of caffeine to alleviate behavioral deficits and cerebellar neuropathology in transgenic mice with a severe ataxia resulting from expression of a truncated fragment of polyglutamine‐expanded ataxin‐3 in Purkinje cells.
Online energy-aware I/O device scheduling for hard real-time systems

Much research has focused on power conservation for the processor, while power conservation for I/O devices has received little attention. In this paper, we analyze the problem of online energy-aware I/O scheduling for hard real-time systems based on the preemptive periodic task model. We propose an online energy-aware I/O device scheduling algorithm: energy-efficient device scheduling (EEDS). The EEDS algorithm utilizes device slack to perform device power state transitions to save energy, without jeopardizing temporal correctness. An evaluation of the approach shows that it yields significant energy savings with respect to no dynamic power management (DPM) techniques
PERCEPTION OF TEACHER EMOTIONAL SUPPORT AND PARENTAL EDUCATION LEVEL: THE IMPACTS ON STUDENTS' MATH PERFORMANCE

There is a paucity of research juxtaposing parental education level and teacher emotional support in a single study which examines their relative impacts on students’ academic achievements. Therefore, the first objective of this dissertation is to study the influence of parental education level, in comparison to the influence of teacher emotional support, on students’ math performance, by using more representative data and a rigorous statistical method. The second objective is to identify and examine how some important psychological traits (both affective and cognitive) mediate the effects of social factors on students’ math performance. The third objective is to examine whether those relationships are moderated by gender. Hong Kong’s survey data is extracted from the Program of International Students Assessment (2003) as organized by Organization for Economic Co-operation and Development (OECD), on the math performances of 4,478 students at the age of fifteen. Measurement invariance was first tested, and then followed by Confirmatory Factor Analysis. Two structural models were tested by Structural Equation Modeling using Linear Structural Relations (LISREL) 8.5 which is computer software for SEM. Results indicated that first, parental education level affects children’s math scores by providing home education resources and enhancing children’s math self-efficacy, and second the Self Determination Theory is applicable in supporting the hypothesis that teachers affects their students’ math scores by providing a cooperative learning environment, which in turn, enhances students’ affective and cognitive factors. Three important mediators, namely cooperative learning environment, math self-efficacy, and home education resources are concluded as significant mediating factors upon the effects of parents and teachers on students’ math performance. The perceived support from parents and teachers are not significantly different across gender in Hong Kong. This is consistent with recent studies that differences favoring males in mathematics achievement are disappearing. Theoretical contributions and practical implications are discussed in the final part of the dissertation.
Escherichia coli mutants with defects in the biosynthesis of 5-methylaminomethyl-2-thio-uridine or 1-methylguanosine in their tRNA

Two tRNA methyltransferase mutants, isolated as described in the accompanying paper (G.R. Björk and K. Kjellin-Stråby, J. Bacteriol. 133:499-207, 1978), are biochemicaaly and genetically characterized. tRNA from mutant IB13 lacks 5-methylaminomethyl-2-thio-uridine in vivo due to a permanently nonfunctional methyltransferase. Thus tRNA from this mutant is a specific substrate for the corresponding tRNA methyltransferase in vitro. In spite of this defect in tRNA, such a mutant is viable. Mutant IB11 is conditionally defective in the biosynthesis of 1-methylguanosine in tRNA due to a temperature-sensitive tRNA (1-methyl-guanosine) methyltransferase. In mutant cells grown at a high temperature, the level of 1-methylguanosine in bulk tRNA is 20% of that of the wild type, demonstrating that in this mutant an 80% deficiency of 1-methylguanosine in tRNA is not lethal. Genetically these two distinct lesions, trmC2, causing 5=methylaminomethyl-2-thio-uridine deficiency, and trmD1, giving a temperature-sensitive tRNA (1-methylguanosine)methyltransferase, are both located between 50 and 61 min on the Escherichia coli chromosome.
Feeling the future: A meta-analysis of 90 experiments on the anomalous anticipation of random future events

In 2011, one of the authors (DJB) published a report of nine experiments in the Journal of Personality and Social Psychology purporting to demonstrate that an individual’s cognitive and affective responses can be influenced by randomly selected stimulus events that do not occur until after his or her responses have already been made and recorded, a generalized variant of the phenomenon traditionally denoted by the term precognition. To encourage replications, all materials needed to conduct them were made available on request. We here report a meta-analysis of 90 experiments from 33 laboratories in 14 countries which yielded an overall effect greater than 6 sigma, z = 6.40, p = 1.2 × 10 -10 with an effect size (Hedges’ g) of 0.09. A Bayesian analysis yielded a Bayes Factor of 5.1 × 10 9, greatly exceeding the criterion value of 100 for “decisive evidence” in support of the experimental hypothesis. When DJB’s original experiments are excluded, the combined effect size for replications by independent investigators is 0.06, z = 4.16, p = 1.1 × 10 -5, and the BF value is 3,853, again exceeding the criterion for “decisive evidence. ” The number of potentially unretrieved experiments required to reduce the overall effect size of the complete database to a trivial value of 0.01 is 544, and seven of eight additional statistical tests support the conclusion that the database is not significantly compromised by either selection bias or by intense “ p-hacking”—the selective suppression of findings or analyses that failed to yield statistical significance. P-curve analysis, a recently introduced statistical technique, estimates the true effect size of the experiments to be 0.20 for the complete database and 0.24 for the independent replications, virtually identical to the effect size of DJB’s original experiments (0.22) and the closely related “presentiment” experiments (0.21). We discuss the controversial status of precognition and other anomalous effects collectively known as psi.
SpamGuru: An Enterprise Anti-Spam Filtering System

Spam-reduction techniques have developed rapidly over the last few years, as spam volumes have increased. We believe that no one anti-spam solution is the “right” answer, and that the best approach is a multifaceted one, combining various forms of filtering with infrastructure changes, financial changes, legal recourse, and more, to provide a stronger barrier to spam than can be achieved with one solution alone. SpamGuru addresses the part of this multi-faceted approach that can be handled by technology on the recipient’s side, using plug-in tokenizers and parsers, plug-in classification modules, and machine-learning techniques to achieve high hit rates and low false-positive rates.
Gain-scheduled compensation for time delay of bilateral teleoperation systems

In this study, the design of controllers for the master-slave system is discussed on the basis of the H/sub /spl infin//-optimal control theory. A few controllers that achieve given performance specifications for the free motion and the constrained motion are designed in order. Especially, by considering a variation of time delay, a time-varying controller incorporates to adjust to the current time delay is designed in the framework of the gain scheduling. This control strategy typically achieves higher performance in the face of large variations in operating conditions. The effectiveness of proposed method is confirmed by the experiments and the simulations.
Utility Accrual Real-Time Scheduling: Models and Algorithms

This dissertation first presents an uniprocessor real-time scheduling algorithm called the Gbeneric Bbenefit Sbcheduling algorithm (or GBS). GBS solves a previously open real-time scheduling problem: scheduling activities subject to arbitrarily shaped, time/utility function (TUF) time constraints and mutual exclusion resource constraints. A TUF specifies the utility of completing an application activity as an application- or situation-specific function of when that activity completes. GBS considers the scheduling objective of maximizing system-wide, total accrued utility, while respecting mutual exclusion constraints. Since this problem is NP -hard, GBS heuristically computes schedules in polynomial-time. The performance of the GBS algorithm is evaluated through simulation and through an implementation on a Portable Operating System Interface (POSIX)-compliant real-time operating system. The simulation studies and implementation measurements reveal that GBS performs close to, if not better than existing algorithms for the cases that they apply. Further, the results verify the effectiveness of GBS for its unique model. We also analytically establish timeliness and non-timeliness properties of GBS including bounds on activity utilities and mutual exclusion. GBS targets real-time systems that are subject to significant non-determinism inherent in their operating environments e.g., completely unknown activity arrivals. When system uncertainties can be stochastically characterized (e.g., stochastic activity arrivals and execution times), it is possible to provide stochastic assurances on timeliness behavior. The dissertation also presents algorithmic solutions to fundamental assurance problems in TUF-driven real-time systems, including stochastically satisfying individual, activity utility lower bounds and system-wide, total utility lower bounds. The algorithmic solutions include algorithms for processor bandwidth allocation and TUF scheduling. While bandwidth allocation algorithms allocate processor bandwidth share to activities to satisfy utility lower bounds, TUF scheduling algorithms schedule activities to maximize accrued utility. The algorithmic solutions and analysis are extended with a class of lock-free and lock-based resource access protocols to satisfy mutual exclusion constraints. We show that satisfying utility lower bounds with lock-based resource access protocols does not imply doing so with the lock-free scheme, and vice versa. Finally, the dissertation presents a rule-based framework for trading off assurance requirements on utility lower bound satisfaction. * *This work is partially supported by the U.S. Office of Naval Research (ONR) under Grant N00014-99-1-0158 and N00014-00-1-0549, the MITRE Corporation under Grant 52917, and the QNX Software Systems Ltd. (SSL) through a software grant. The views and conclusions contained in this document are those of the author and should not be interpreted as representing the official policies, either expressed or implied, of ONR, MITRE, or QNX SSL.
A Novel Cyclophilin B Gene in the Red Tide Dinoflagellate Cochlodinium polykrikoides: Molecular Characterizations and Transcriptional Responses to Environmental Stresses

The marine dinoflagellate Cochlodinium polykrikoides is one of the most common ichthyotoxic species that causes harmful algal blooms (HABs), which leads to ecological damage and huge economic loss in aquaculture industries. Cyclophilins (CYPs) belong to the immunophilin superfamily, and they may play a role in the survival mechanisms of the dinoflagellate in stress environments. In the present study, we identified a novel cyclophilin gene from C. polykrikoides and examined physiological and gene transcriptional responses to biocides copper sulphate (CuSO4) and sodium hypochlorite (NaOCl). The full length of CpCYP was 903 bp, ranging from the dinoflagellate splice leader (DinoSL) sequence to the polyA tail, comprising a 639 bp ORF, a 117 bp 5′-UTR, and a 147 bp 3′-UTR. Motif and phylogenetic comparisons showed that CpCYP was affiliated to group B of CYP. In biocide stressors, cell counts, chlorophyll a, and photosynthetic efficiency (Fv/Fm) of C. polykrikoides were considerably decreased in both exposure time- and dose-dependent manners. In addition, CpCYP gene expression was significantly induced after 24 h exposure to the biocide-treated stress conditions. These results indicate an effect of the biocides on the cell physiology and expression profile of CpCYP, suggesting that the gene may play a role in environmental stress responses.
Heart Rate and Extracellular Sodium and Potassium Modulation of Gap Junction Mediated Conduction in Guinea Pigs

Background: Recent studies suggested that cardiac conduction in murine hearts with narrow perinexi and 50% reduced connexin43 (Cx43) expression is more sensitive to relatively physiological changes of extracellular potassium ([K+]o) and sodium ([Na+]o). Purpose: Determine whether similar [K+]o and [Na+]o changes alter conduction velocity (CV) sensitivity to pharmacologic gap junction (GJ) uncoupling in guinea pigs. Methods: [K+]o and [Na+]o were varied in Langendorff perfused guinea pig ventricles (Solution A: [K+]o = 4.56 and [Na+]o = 153.3 mM. Solution B: [K+]o = 6.95 and [Na+]o = 145.5 mM). Gap junctions were inhibited with carbenoxolone (CBX) (15 and 30 μM). Epicardial CV was quantified by optical mapping. Perinexal width was measured with transmission electron microscopy. Total and phosphorylated Cx43 were evaluated by western blotting. Results: Solution composition did not alter CV under control conditions or with 15μM CBX. Decreasing the basic cycle length (BCL) of pacing from 300 to 160 ms decreased CV uniformly with both solutions. At 30 μM CBX, a change in solution did not alter CV either longitudinally or transversely at BCL = 300 ms. However, reducing BCL to 160 ms caused CV to decrease more in hearts perfused with Solution B than A. Solution composition did not alter perinexal width, nor did it change total or phosphorylated serine 368 Cx43 expression. These data suggest that the solution dependent CV changes were independent of altered perinexal width or GJ coupling. Action potential duration was always shorter in hearts perfused with Solution B than A, independent of pacing rate and/or CBX concentration. Conclusions: Increased heart rate and GJ uncoupling can unmask small CV differences caused by changing [K+]o and [Na+]o. These data suggest that modulating extracellular ionic composition may be a novel anti-arrhythmic target in diseases with abnormal GJ coupling, particularly when heart rate cannot be controlled.
Sustainable production of azadirachtin from differentiated in vitro cell lines of neem (Azadirachta indica)

Neem possesses immense medicinal properties and has immediate application as ecofriendly, biodegradable biopesticide. All these properties are because of a structurally complex bioactive compound Azadirachtin, mainly present in seeds. However, it could not be exploited to its full because of heterogeneity in compound production due to out-breeding in nature of the plant. This is the first elaborate report on systematic studies on azadirachtin biosynthesis where different redifferentiated and dedifferentiated in vitro cell lines of A. indica (neem), obtained from various explants, were utilized. All cell lines were found positive for the compound with significantly higher azadirachtin yield of 2330 µg /g DW was obtained from redifferentiated cell lines established from zygotic embryo cultures. The study, demonstrates the possibility of consistent biosynthesis of azadirachtin in bulk under optimal growth conditions.
LATE BRONZE AGE METAL FINDS IN THE POŽEGA VALLEY

The Požega Valley is a distinct geographic unit in the central portion of northern Croatia. Its strategic location between the vital courses of the Sava and Drava rivers accords this region with exceptional importance as a communications zone, which is confirmed by the numerous archaeological finds dating from prehistory to the Middle Ages. Therefore, the important finds dating to the Late Bronze Age are not surprising. Since bronze metallurgy expanded considerably during that era, metal finds are very numerous in the Požega Valley. Most often they appear as hoards or individual finds, while more rarely they are found within the context of settlements or graves. The category of Late Bronze Age metal finds from the Požega Valley consists of weapons, tools and jewelry which at some point were buried either individually or jointly as hoards, and they can be dated to periods from Ha A to Ha B.