Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

The central questions of bacterial ecology and evolution require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles (ecotypes). Because of a lack of theory-based guidelines, current methods in bacterial systematics fail to divide the bacterial domain of life into meaningful units of ecology and evolution. We introduce a sequence-based approach (“ecotype simulation”) to model the evolutionary dynamics of bacterial populations and to identify ecotypes within a natural community, focusing here on two Bacillus clades surveyed from the “Evolution Canyons” of Israel. This approach has identified multiple ecotypes within traditional species, with each predicted to be an ecologically distinct lineage; many such ecotypes were confirmed to be ecologically distinct, with specialization to different canyon slopes with different solar exposures. Ecotype simulation provides a long-needed natural foundation for microbial ecology and systematics.
“The Art of Knowing”: Social and Tacit Dimensions of Knowledge and the Limits of the Community of Practice

Community of practice theory is inherently a social theory. As such it is distinct from more individualist accounts of human behavior, such as mainstream economics. Consequently, community of practice theory and economics favor different accounts of knowledge. Taking a community of practice perspective, this article challenges economists' attempts to reduce knowledge to information held by individuals and to reject tacit knowledge as mere uncodified explicit knowledge. The essay argues that Polanyi's notion of a tacit dimension affected numerous disciplines (including economics) because it addressed aspects of learning and identity that conventional social sciences overlooked. The article situates knowledge, identity, and learning within communities and points to ethical and epistemic entailments of community practice. In so doing it attempts to limit, rather than expand, the scope of community of practice analysis and to stress the difference, rather than the commonalities, between this and other apparently congenial forms of social analysis.
A Robust Gradient Sampling Algorithm for Nonsmooth, Nonconvex Optimization

Let f be a continuous function on $\Rl^n$, and suppose f is continuously differentiable on an open dense subset. Such functions arise in many applications, and very often minimizers are points at which f is not differentiable. Of particular interest is the case where f is not convex, and perhaps not even locally Lipschitz, but is a function whose gradient is easily computed where it is defined. We present a practical, robust algorithm to locally minimize such functions, based on gradient sampling. No subgradient information is required by the algorithm. When f is locally Lipschitz and has bounded level sets, and the sampling radius $\eps$ is fixed, we show that, with probability 1, the algorithm generates a sequence with a cluster point that is Clarke $\eps$-stationary. Furthermore, we show that if f has a unique Clarke stationary point $\bar x$, then the set of all cluster points generated by the algorithm converges to $\bar x$ as $\eps$ is reduced to zero. Numerical results are presented demonstrating the robustness of the algorithm and its applicability in a wide variety of contexts, including cases where f is not locally Lipschitz at minimizers. We report approximate local minimizers for functions in the applications literature which have not, to our knowledge, been obtained previously. When the termination criteria of the algorithm are satisfied, a precise statement about nearness to Clarke $\eps$-stationarity is available. A MATLAB implementation of the algorithm is posted at http://www.cs. nyu.edu/overton/papers/gradsamp/alg.
Dimethylglycine Provides Salt and Temperature Stress Protection to Bacillus subtilis

ABSTRACT Glycine betaine is a potent osmotic and thermal stress protectant of many microorganisms. Its synthesis from glycine results in the formation of the intermediates monomethylglycine (sarcosine) and dimethylglycine (DMG), and these compounds are also produced when it is catabolized. Bacillus subtilis does not produce sarcosine or DMG, and it cannot metabolize these compounds. Here we have studied the potential of sarcosine and DMG to protect B. subtilis against osmotic, heat, and cold stress. Sarcosine, a compatible solute that possesses considerable protein-stabilizing properties, did not serve as a stress protectant of B. subtilis. DMG, on the other hand, proved to be only moderately effective as an osmotic stress protectant, but it exhibited good heat stress-relieving and excellent cold stress-relieving properties. DMG is imported into B. subtilis cells primarily under osmotic and temperature stress conditions via OpuA, a member of the ABC family of transporters. Ligand-binding studies with the extracellular solute receptor (OpuAC) of the OpuA system showed that OpuAC possesses a moderate affinity for DMG, with a Kd value of approximate 172 μM; its Kd for glycine betaine is about 26 μM. Docking studies using the crystal structures of the OpuAC protein with the sulfur analog of DMG, dimethylsulfonioacetate, as a template suggest a model of how the DMG molecule can be stably accommodated within the aromatic cage of the OpuAC ligand-binding pocket. Collectively, our data show that the ability to acquire DMG from exogenous sources under stressful environmental conditions helps the B. subtilis cell to cope with growth-restricting osmotic and temperature challenges.
In Vitro and In Vivo Neurotoxicity of Prion Protein Oligomers

The mechanisms underlying prion-linked neurodegeneration remain to be elucidated, despite several recent advances in this field. Herein, we show that soluble, low molecular weight oligomers of the full-length prion protein (PrP), which possess characteristics of PrP to PrPsc conversion intermediates such as partial protease resistance, are neurotoxic in vitro on primary cultures of neurons and in vivo after subcortical stereotaxic injection. Monomeric PrP was not toxic. Insoluble, fibrillar forms of PrP exhibited no toxicity in vitro and were less toxic than their oligomeric counterparts in vivo. The toxicity was independent of PrP expression in the neurons both in vitro and in vivo for the PrP oligomers and in vivo for the PrP fibrils. Rescue experiments with antibodies showed that the exposure of the hydrophobic stretch of PrP at the oligomeric surface was necessary for toxicity. This study identifies toxic PrP species in vivo. It shows that PrP-induced neurodegeneration shares common mechanisms with other brain amyloidoses like Alzheimer disease and opens new avenues for neuroprotective intervention strategies of prion diseases targeting PrP oligomers.
The upper limbs after stroke : exploring effects of bilateral training and determinants of recovery

Background: Bilateral task training (BT) may improve upper limb (UL) recovery on the affected as well as non-affected side in longstanding stroke however for acute stroke its effects on physical and psychosocial outcomes compared to unilateral training (UT) has not been clearly established. Furthermore, clinical and demographic factors that influence UL training responses and predict UL recovery are also unclear for acute stroke. PrimaryAims: To compare effects of BT and UT on: • ipsilesional and contralesional UL outcomes • anxiety, depression and health related quality of life (HRQOL) Secondary Aims: To investigate: • which clinical and demographic factors influence contralesional training responses • predictors of UL activity limitation over time for the sample as a whole • UL dysfunction as a predictor of HRQOL six months after stroke for the sample as a whole Design: Single-blinded randomised controlled trial, with outcome assessment at baseline (T1), after 6 weeks training (T2), and 18 week follow-up (T3). Participants: 106 in-patients randomised to receive BT (n=56) or UT (n=50) 2 to 4 weeks after stroke onset. Intervention: Supervised BT or UT for 20 minutes on 5 weekdays, over 6 weeks, using a standardised programme developed for the study. Outcome Measures: UL outcomes: Action Research Arm Test (ARAT), Rivermead Motor Assessment (UL scale), Nine-Hole Peg Test (9HPT). Secondary measures: Modified Barthel Index, Hospital Anxiety and Depression Scale, and Nottingham Health Profile. Assessment was conducted by a blinded assessor. Results: Between the two groups, there were no significant differences at T1 or T2 on any contralesional UL measure or on any psychosocial measure (p>0.05). At T3, 9HPT (p=0.03) and ARAT pinch section scores (p=0.04) in the UT group were significantly higher. None of the selected clinical or demographic factors significantly influenced training responses. BT significantly improved ipsilesional dexterity between T1 and T2 (p=0.04). For the sample as a whole, early ARAT and MBI scores significantly predicted contralesional ARAT scores at T2 and T3. Anxiety, depression and UL impairment significantly predicted overall HRQOL at T3. Conclusions: BT was no more effective than UT for the affected arm – in fact UT was more effective for dexterity. BT was more effective than UT, however, for short-term recovery of ipsilesional dexterity. Future studies should determine optimal BT characteristics for contraand ipsilesional recovery in stroke populations with differing levels of severity. Knowledge of predictors of UL activity limitation and HRQOL will enable therapists to target rehabilitation at factors that most influence these important outcomes.
Personal Agent for Services in ITS

In this paper, we introduce the concept of a privacy enhancing personal agent that manages a user's privacy policy settings and provides access control functions to ITS services. The personal agent acts as a proxy between a vehicle and service providers, and it automatically decides whether personal data can be sent to a service provider based on the privacy policy settings. The functions of the personal agent are also described. The personal agent provides a common web-based interface, and the quality of data can be controlled through anonymization levels. Our research provides a conceptual model of the personal agent and considers the design of the personal agent based on privacy requirements. Drivers can delegate their user consent role to the personal agent by configuring privacy policy settings on the personal agent. The personal agent is a key component for achieving a secure and reliable data transfer platform between vehicles and service providers.
Japan's Deflation, Problems in the Financial System and Monetary Policy

On 18-19 June 2004, the BIS held a conference on "Understanding Low Inflation and Deflation". This event brought together central bankers, academics and market practitioners to exchange views on this issue (see the conference programme in this document). This paper was presented at the workshop. The views expressed are those of the author(s) and not those of the BIS.
Analysis of TBX1 Variation in Patients with Psychotic and Affective Disorders

A significant portion of patients with 22q11 deletion syndrome (22q11DS) develop psychiatric disorders, including schizophrenia and other psychotic and affective symptoms, and the responsible gene/s are assumed to also play a significant role in the etiology of nonsyndromic psychiatric disease. The most common psychiatric diagnosis among patients with 22q11DS is schizophrenia, thought to result from neurotransmitter imbalances and also from disturbed brain development. Several genes in the 22q11 region with known or suspected roles in neurotransmitter metabolism have been analyzed in patients with isolated schizophrenia; however, their contribution to the disease remains controversial. Haploinsufficiency of the TBX1 gene has been shown to be sufficient to cause the core physical malformations associated with 22q11DS in mice and humans and via abnormal brain development could contribute to 22q11DS-related and isolated psychiatric disease. 22q11DS populations also have increased rates of psychiatric conditions other than schizophrenia, including mood disorders. We therefore analyzed variations at the TBX1 locus in a cohort of 446 white patients with psychiatric disorders relevant to 22q11DS and 436 ethnically matched controls. The main diagnoses included schizophrenia (n = 226), schizoaffective disorder (n = 67), bipolar disorder (n = 82), and major depressive disorder (n = 29). We genotyped nine tag SNPs in this sample but did not observe significant differences in allele or haplotype frequencies in any of the analyzed groups (all affected, schizophrenia and schizoaffective disorder, schizophrenia alone, and bipolar disorder and major depressive disorder) compared with the control group. Based on these results we conclude that TBX1 variation does not make a strong contribution to the genetic etiology of nonsyndromic forms of psychiatric disorders commonly seen in patients with 22q11DS.
Aggregating Bandwidth for Multihomed Mobile Collaborative Communities

Multihomed, mobile wireless computing and communication devices can spontaneously form communities to logically combine and share the bandwidth of each other's wide-area communication links using inverse multiplexing. But, membership in such a community can be highly dynamic, as devices and their associated WWAN links randomly join and leave the community. We identify the issues and trade-offs faced in designing a decentralized inverse multiplexing system in this challenging setting and determine precisely how heterogeneous WWAN links should be characterized and when they should be added to, or deleted from, the shared pool. We then propose methods of choosing the appropriate channels on which to assign newly arriving application flows. Using video traffic as a motivating example, we demonstrate how significant performance gains can be realized by adapting allocation of the shared WWAN channels to specific application requirements. Our simulation and experimentation results show that collaborative bandwidth aggregation systems are, indeed, a practical and compelling means of achieving high-speed Internet access for groups of wireless computing devices beyond the reach of public or private access points
Self-Similar Solutions of Bianchi Type iii SpaceTimes Using Partial Differential Equations

A different approach is developed to study self-similar solutions in Bianchi type III spacetimes. Self-similar solutions in both tilted and non tilted cases are obtained. By solving a system of six non linear and inhomogeneous partial differential equations. It is shown that in non-tilted case the above space-times admit orthogonal zero kind self-similarity and in tilted case. It admits second and infinite kind self-similarities
The Globalization of Values A Comparison of the United States and the Kingdom of Jordan

Globalization is creating similar environments for younger consumers around the world. With younger individuals being socialized in more similar environments than their parents, the former should have more comparable values than the latter. The goal of the current study was to empirically test this argument. Based on data gathered from 120 subjects across two countries, the results support growing similarities in values between younger consumers in comparison to older consumers. These results suggest that marketers might be able to adopt standardized marketing practices with younger individuals, whereas standardization might not have been an option with their parents.
Blocking of Person Information in Small Social Groupings: The Information of Person Categories.

Abstract : Information about others in one's immediate social environment is encountered sequentially over time. A great deal of variability exists over different social groupings in the patterning of this information. The information may be completely blocked by person (i.e., the information about each person is received in a single, uninterrupted blocked), completely random by person (i.e., the information about each person is interspersed among items about others in the group), or anywhere in between. Sequential blocking was varied continuously from complete person blocking (100%) to chance blocking (0%) in the present study. Also included in the present study were two variables designed to increase the salience of persons as organizing categories. The results of the present study revealed that increases in the degree of person blocking of the stimulus input led to a linear increase in the extent to which the information received by subjects about other persons was organized according to person categories. Blocking was alos shown to affect the subjects' recall of the stimulus items. The relative viability of two competing theoretical explanations for the blocking results are discussed along with the implications of the present results for current theoretical and empirical orientations toward impression formation research. (Author)
Comparing Attribute Classifiers for Interactive Language Grounding

We address the problem of interactively learning perceptually grounded word meanings in a multimodal dialogue system. We design a semantic and visual processing system to support this and illustrate how they can be integrated. We then focus on comparing the performance (Precision, Recall, F1, AUC) of three state-of-the-art attribute classifiers for the purpose of interactive language grounding (MLKNN, DAP, and SVMs), on the aPascal-aYahoo datasets. In prior work, results were presented for object classification using these methods for attribute labelling, whereas we focus on their performance for attribute labelling itself. We find that while these methods can perform well for some of the attributes (e.g. head, ears, furry) none of these models has good performance over the whole attribute set, and none supports incremental learning. This leads us to suggest directions for future work.
Assessing Psychological Distress Near the End of Life

Psychological suffering is one of the most significant and potentially remediable impediments to the dying process for terminally ill patients and their families. This article reviews several of the most common psychological disorders that arise in the context of terminal illness, including depression, anxiety, delirium, and suicidal ideation. Issues related to assessment, measurement, and differential diagnosis are reviewed.
Hybrid Link Adaptation for ICI Adjustment in OFDMA Cellular Uplink Systems

In orthogonal frequency division multiple access (OFDMA)-based uplink systems, it may not be feasible to exploit the rate adaptation due to severe intercarrier interference (ICI). In this paper, we propose a novel hybrid link adaptation scheme that employs power adaptation for ICI adjustment and rate adaptation for capacity improvement in OFDMAbased uplink systems. The proposed scheme determines the maximum allowable transmit power in response to the channel gain and mobility of the user, guaranteeing the carrier to interference power ratio (CIR) loss of all users.
7-tert-Butyl-6-(4-Chloro-Phenyl)-2-Thioxo-2,3-Dihydro-1H-Pyrido[2,3-d]Pyrimidin-4-One, a Classic Polymodal Inhibitor of Transient Receptor Potential Vanilloid Type 1 with a Reduced Liability for Hyperthermia, Is Analgesic and Ameliorates Visceral Hypersensitivity

The therapeutic potential of transient receptor potential vanilloid type 1 (TRPV1) antagonists for chronic pain has been recognized for more than a decade. However, preclinical and clinical data revealed that acute pharmacological blockade of TRPV1 perturbs thermoregulation, resulting in hyperthermia, which is a major hurdle for the clinical development of these drugs. Here, we describe the properties of 7-tert-butyl-6-(4-chloro-phenyl)-2-thioxo-2,3-dihydro-1H-pyrido[2,3-d]pyrimidin-4-one (BCTP), a TRPV1 antagonist with excellent analgesic properties that does not induce significant hyperthermia in rodents at doses providing maximal analgesia. BCTP is a classic polymodal inhibitor of TRPV1, blocking activation of the human channel by capsaicin and low pH with IC50 values of 65.4 and 26.4 nM, respectively. Similar activity was observed with rat TRPV1, and the inhibition by BCTP was competitive and reversible. BCTP also blocked heat-induced activation of TRPV1. In rats, the inhibition of capsaicin-induced mechanical hyperalgesia was observed with a D50 value of 2 mg/kg p.o. BCTP also reversed visceral hypersensitivity and somatic inflammatory pain, and using a model of neuropathic pain in TRPV1 null mice we confirmed that its analgesic properties were solely through the inhibition of TRPV1. We were surprised to find that BCTP administered orally induced only a maximal 0.6°C increase in core body temperature at the highest tested doses (30 and 100 mg/kg), contrasting markedly with N-[4-({6-[4-(trifluoromethyl)phenyl]pyrimidin-4-yl}oxy)-1,3-benzothiazol-2-yl]acetamide (AMG517), a clinically tested TRPV1 antagonist, which induced marked hyperthermia (>1°C) at doses eliciting submaximal reversal of capsaicin-induced hyperalgesia. The combined data indicate that TRPV1 antagonists with a classic polymodal inhibition profile can be identified where the analgesic action is separated from the effects on body temperature.
Learning to address multiple syndemics for people living with HIV through client perspectives on CBT

Abstract Objective: The mental health burden among people living with HIV/AIDS (PLWHA) is high and often involves multiple comorbid psychological and substance use-related psychosocial problems. These co-occurring problems, or syndemics, additively impair engagement in HIV disease management. Existing psychotherapies for mental health and HIV health have generally focused on a single psychosocial problem and little research exists to guide future psychotherapies that address multiple mental health issues. Method: To address this gap in understanding, we conducted qualitative interviews with multiply comorbid PLWHA (N = 30) who completed cognitive-behavioural therapy (CBT) for depression and medication adherence. Results: Themes emerged regarding participants’ perspectives on how overlapping substance use and mood disorders interacted to reduce the benefit of CBT. Substance use was a dominant theme compared to other syndemics, highlighting the need for integrated mental health and substance use interventions. Interviews also suggested modifications of which psychosocial concerns participants felt should be prioritized in treatment delivery. Finally, participants described content they would want in a psychotherapy intervention, including intimacy and sexual health. Conclusions: Future psychotherapeutic interventions for syndemic problems and HIV self-care will need to comprehensively address complex concerns, including issues salient to the overall well-being of PLWHA. This may improve client engagement and, ultimately, mental, and physical health outcomes. Clinical or methodological significance of this article: Although mental health comorbidity is common and often complex among clients living with HIV, little research exists to guide psychotherapy for such intricate mental health concerns. The current study used content analysis of in-depth qualitative interviews with clients living with HIV and multiple mental health comorbidities who had recently completed cognitive-behavioural therapy. Recommendations based on these findings suggest strategies for clinicians working with similar clients to consider and offers suggestions for future treatment development research.