Miracle-dz/UniFAR-FTUs huggingface dataset:
Adverse events associated with testosterone replacement in middle-aged and older men: a meta-analysis of randomized, placebo-controlled trials.

BACKGROUND We performed a meta-analysis of randomized clinical trials to determine the risks of adverse events associated with testosterone replacement in older men. METHODS The MEDLINE database was searched from 1966 to April 2004, using testosterone as the indexing term; limits included human, male, > or =45 years old, and randomized controlled trial. Of the 417 studies thus identified, 19 met the inclusion criteria: testosterone replacement for at least 90 days, men > or =45 years old with low or low-normal testosterone level, randomized controlled trial, and medically stable men. Odds ratios (ORs) were pooled using a random effects model, assuming heterogeneous results across studies, and were weighted for sample size. RESULTS In the 19 studies that met eligibility criteria, 651 men were treated with testosterone and 433 with placebo. The combined rate of all prostate events was significantly greater in testosterone-treated men than in placebo-treated men (OR = 1.78, 95% confidence interval [CI], 1.07-2.95). Rates of prostate cancer, prostate-specific antigen (PSA) >4 ng/ml, and prostate biopsies were numerically higher in the testosterone group than in the placebo group, although differences between the groups were not individually statistically significant. Testosterone-treated men were nearly four times as likely to have hematocrit >50% as placebo-treated men (OR = 3.69, 95% CI, 1.82-7.51). The frequency of cardiovascular events, sleep apnea or death was not significantly different between the two groups. CONCLUSIONS Testosterone replacement in older men was associated with a significantly higher risk of detection of prostate events and of hematocrit >50% than was placebo; hematocrit increase was the most frequent adverse event associated with testosterone replacement. These data reaffirm the need to monitor hematocrit, PSA, and digital examination of the prostate during testosterone replacement in older men.
Pharos: Collating protein information to shed light on the druggable genome

The ‘druggable genome’ encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental techniques and a Knowledge Management Center (KMC) that would collect and organize information about protein targets from four families, representing the most common druggable targets with an emphasis on understudied proteins. Here, we describe two resources developed by the KMC: the Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos (https://pharos.nih.gov), a multimodal web interface that presents the data from TCRD. We briefly describe the types and sources of data considered by the KMC and then highlight features of the Pharos interface designed to enable intuitive access to the IDG knowledgebase. The aim of Pharos is to encourage ‘serendipitous browsing’, whereby related, relevant information is made easily discoverable. We conclude by describing two use cases that highlight the utility of Pharos and TCRD.
Neuronal population coding of continuous and discrete quantity in the primate posterior parietal cortex

Quantitative knowledge guides vital decisions in the life of animals and humans alike. The posterior parietal cortex in primates has been implicated in representing abstract quantity, both continuous (extent) and discrete (number of items), supporting the idea of a putative generalized magnitude system in this brain area. Whether or not single neurons encode different types of quantity, or how quantitative information is represented in the neuronal responses, however, is unknown. We show that length and numerosity are encoded by functionally overlapping groups of parietal neurons. Using a statistical classifier, we found that the activity of populations of quantity-selective neurons contained accurate information about continuous and discrete quantity. Unexpectedly, even neurons that were nonselective according to classical spike-count measures conveyed robust categorical information that predicted the monkeys' quantity judgments. Thus, different information-carrying processes of partly intermingled neuronal networks in the parietal lobe seem to encode various forms of abstract quantity.
Identifying Scattering Obstacles by the Construction of Nonscattering Waves

There are many methods for identifying the shape and location of scatterers from far field data. We take the view that the connections between algorithms are more illuminating than their differences, particularly with regard to the linear sampling method [D. Colton and A. Kirsch, Inverse Problems, 12 (1996), pp. 383–393], the point source method [R. Potthast, Point Sources and Multipoles in Inverse Scattering Theory, Chapman & Hall, London, UK, 2001], and the MUSIC algorithm [A. J. Devaney, IEEE Trans. Antennas and Propagation, 53 (2005), pp. 1600–1610]. Using the first two techniques we show that, for a scatterer with Dirichlet boundary conditions, there is a nontrivial incident field that does not generate a scattered field. This incident field, written as an expansion of eigenfunctions of the far field operator, is used in the MUSIC algorithm to image the shape and location of the obstacle as those points z where the incident field is orthogonal to the far field pattern due to a point source located at.
Mixed visual reference frames: perceiving nonretino-centric visual quantities in a retino-centric frame

It is a useful competence to see motion relative to the head or to the external world, although those quantities are not directly given on the retina. The same holds for judgement of the shape of an object. We argue that the required transformations can be, and are done independent of the associated direction transformations. This involves perceptual channels with retinal apertures but non-retinocentric motion- or shape- sensitivity. In order to arrive at units that perform such a mixed transformation, the substructure of the retinotopic receptive field needs to be dynamically adjusted, using extra-retinal signals (or equivalent measures like vertical disparity). Here we show that detectors tuned to disparity-curvature X retinal-direction can extract (metric) object curvature from the retinal disparity field in one step. We point out the correspondence to a previously proposed model of heading detection, which contains detectors that become tuned to head-centric flow by dynamically changing their preferred structure of the flowfield in a retinal aperture, depending on the eye movement.
Beyond Alhazen's problem: Analytical projection model for non-central catadioptric cameras with quadric mirrors

Catadioptric cameras are widely used to increase the field of view using mirrors. Central catadioptric systems having an effective single viewpoint are easy to model and use, but severely constraint the camera positioning with respect to the mirror. On the other hand, non-central cata-dioptric systems allow greater flexibility in camera placement, but are often approximated using central or linear models due to the lack of an exact model. We bridge this gap and describe an exact projection model for non-central catadioptric systems. We derive an analytical ‘forward projection’ equation for the projection of a 3D point reflected by a quadric mirror on the imaging plane of a perspective camera, with no restrictions on the camera placement, and show that it is an 8th degree equation in a single unknown. While previous non-central catadioptric cameras primarily use an axial configuration where the camera is placed on the axis of a rotationally symmetric mirror, we allow off-axis (any) camera placement. Using this analytical model, a non-central catadioptric camera can be used for sparse as well as dense 3D reconstruction similar to perspective cameras, using well-known algorithms such as bundle adjustment and plane sweeping. Our paper is the first to show such results for off-axis placement of camera with multiple quadric mirrors. Simulation and real results using parabolic mirrors and an off-axis perspective camera are demonstrated.
Detection of Human Papillomavirus Infection and p16 Immunohistochemistry Expression in Bladder Cancer with Squamous Differentiation

Objectives To determine the potential association between HPV infection and the squamous cell component of urothelial carcinoma (UC) of the bladder and to validate p16 overexpression as a surrogate marker for HPV infection in these cancers among Koreans. Methods We analyzed the presence of HPV infection using an HPV-DNA chip and the expression of p16 using immunohistochemistry in 47 subjects between July 2001 and March 2011. The study group (n = 35) included patients with squamous differentiation of UC of the bladder. The control group (n = 12) included patients with squamous metaplasia of the bladder. Results Baseline characteristics of control and study groups were similar. HPV DNA detection rates were approximately 2-fold higher in the study than the control group (17.1% [6/35] versus 8.3% [1/12], respectively), but the difference was not statistically significant. P16 overexpression was detected in 16/35 (45.7%) study group and 1/12 (8.3%) control group samples (p = 0.034). Both HPV-positivity and p16 overexpression were present in 3/35 (8.8%) study group samples, but none of the control group (p = 0.295). In the study group, the percentage of HPV-positive cases who were non-smokers was 2-fold higher than the percentage of HPV-negative cases who were non-smokers (66.7% [4/6] versus 31.0% [9/29], respectively); however, statistical significance was not achieved due to the small sample size. Conclusions HPV infection may be associated with UC of the bladder with squamous differentiation, especially in non-smokers. However, p16 expression does not appear to be a strong surrogate marker for evidence of HPV infection in this type of cancer.
On the virtue of succinct proofs: amplifying communication complexity hardness to time-space trade-offs in proof complexity

An active line of research in proof complexity over the last decade has been the study of proof space and trade-offs between size and space. Such questions were originally motivated by practical SAT solving, but have also led to the development of new theoretical concepts in proof complexity of intrinsic interest and to results establishing nontrivial relations between space and other proof complexity measures. By now, the resolution proof system is fairly well understood in this regard, as witnessed by a sequence of papers leading up to [Ben-Sasson and Nordstrom 2008, 2011] and [Beame, Beck, and Impagliazzo 2012]. However, for other relevant proof systems in the context of SAT solving, such as polynomial calculus (PC) and cutting planes (CP), very little has been known. Inspired by [BN08, BN11], we consider CNF encodings of so-called pebble games played on graphs and the approach of making such pebbling formulas harder by simple syntactic modifications. We use this paradigm of hardness amplification to make progress on the relatively longstanding open question of proving time-space trade-offs for PC and CP. Namely, we exhibit a family of modified pebbling formulas {F_n} such that: - The formulas F_n have size O(n) and width O(1). - They have proofs in length O(n) in resolution, which generalize to both PC and CP. - Any refutation in CP or PCR (a generalization of PC) in length L and space s must satisfy s log L >≈ √[4]{n}. A crucial technical ingredient in these results is a new two-player communication complexity lower bound for composed search problems in terms of block sensitivity, a contribution that we believe to be of independent interest.
Commentary on taxonomic inflation, species delimitation and classification in Ruminantia

The species problem and the debate about species concepts have been shaking up both evolutionary biology and taxonomy for decades or even centuries (Wilkins 2009), but over the last 10 or so years the paradigmatic shift from the biological species concept (BSC) to the phylogenetic species concept(s) (PSC) has added a new dimension to the discussion: taxonomic inflation (Isaac et al. 2004), i. e. the artificial increase of species number of a taxon through splitting, mainly through raising former sub-species to species rank. The debate was initiated in the context of mammalian taxonomy, and a number of studies, commentaries and rejoinders by adherents of the diagnosability version of the PSC and its critics have been published recently In this commentary, I raise some of the discussed points that I consider particularly important and then list a number of recent examples of what I consider excessive splitting of some ruminant species. First of all, it should be made clear that there is nothing wrong with species splitting per se and that taxonomic inflation is not a necessary consequence of splitting. Cryptic diversity and cryptic species are real, and it is also true that many taxa, even among mammals, are understudied and often have not been revised for decades. Thus, the number of species in general and the number of mammal and ruminant species in particular will likely increase for good reasons (some examples of two or more line-ages subsumed under a single species at present or until recently include badgers, clouded leopards, probably African elephants and possibly also giraffe, see Zachos et al. 2013a; but doubtless there are many more). So, my criticism should not be misunderstood as opposed to species splitting in general! We certainly possess only superficial knowledge of the biodiversity in many, if not most groups of organisms , and present species lists are consequently often only the tip of the iceberg. The species we have missed so far will not always be those that we have not yet seen, but perhaps equally often (and probably much more often in the case of mammals) those that we have not yet recognised, i. e. those that are subsumed under a single name with one or more other species (cryptic species). That said, I have serious doubts as to whether the Phylogenetic Species Concept is a scientifically sensible approach to uncovering and taxonomical-ly acknowledging this cryptic diversity. In the case …
Determinants of management errors in acute severe asthma.

BACKGROUND: It is hypothesised that, despite recent initiatives to improve asthma self-management including asthma education, detailed investigation of the sequence of events culminating in hospital admission will lead to the identification of important management errors and thus the likelihood that the majority of severe asthma attacks are preventable by currently available strategies, and that psychological, health care and socioeconomic factors are risk factors for such management errors. METHODS: A cross sectional study was undertaken of 138 patients aged 15-50 years admitted to hospital (general ward or intensive care unit) with acute severe asthma who were assessed within 24-72 hours of admission using a number of previously validated instruments. A detailed history of events of the attack was assessed against predetermined criteria for non or delayed use of oral corticosteroids and non or delayed use of emergency ambulance services. RESULTS: Subjects had evidence of severe chronic asthma and had acute severe asthma at presentation (n = 90, pH = 7.3 (0.2), PaCO2 = 7.2 (5.0) kPa) but duration of hospital stay was short (3.7 (2.6) days). Serious management errors occurred very frequently and most were deemed to have been made by the patient. Forward stepwise regression revealed that delayed or non-use of oral corticosteroids was predicted independently by lack of paying job (p = 0.02), high total use of inhaled beta agonists in the 24 hours before index admission (p = 0.04), loss of a job in the last year (p = 0.04), low frequency of use of oral corticosteroids in the last year (p = 0.06), concerns during the index attack about medical expenses (p = 0.07), and delay in the use of ambulance services (p = 0.05)--the model being responsible for 23% of the variance. Delayed or non-summoning of emergency ambulance services was predicted independently by total life events (p = 0.03), having something stolen in the last year (p = 0.003), panic during the index attack (p = 0.01), and concerns during the index attack about taking time off work (p = 0.07)--the model being responsible for 21% of the variance. CONCLUSIONS: The results of this study show that, despite recent educational advances, serious management errors are common in those admitted to hospital with acute severe asthma and that most management errors relate to patient self-management behaviour. Serious management errors are predicted by a variety of socio-economic and psychological factors. While the results of this study are consistent with the widely held view that most acute severe attacks are theoretically preventable, the challenge for the future is to change patients' behaviour in the face of considerable adverse socioeconomic and psychological factors.
Education, Modern Development, and Indigenous Knowledge: An Analysis of Academic Knowledge Production

This book re-conceptualizes the field of international and comparative education by utilizing indigenous knowledge as a central component for altering the dominant, eurocentric social science research paradigm. Examples from indigenous sources of knowledge are juxtaposed to the dominant discourses on education and modern development in subaltern societies in order to provide scholars with alternative ways of viewing education and development and to shape how subaltern peoples are understood and represented in academic research. Bibliography. Index.
ONLINE BEHAVIOURAL INTENTIONS: AN EMPIRICAL INVESTIGATION OF ANTECEDENTS AND MODERATORS

The objectives of this paper is to recognize, confirm and evaluate the underlying factors toward behavior intention of Indonesian online shoppers; specifically the antecedents including perceived online reputation, banner advertising, perceived online security, perceived reliability, appearance, site design, and website presentational consistency. Questionnaires were posted through online survey targeted to 200 respondents. The data collection methods and variable measures were discussed. Zero-order correlation and regression analysis were conducted to evaluate whether the antecedents and moderator have relationships with the online behavior intention. Analyses found that perceived online security was the only antecedent variable that directly and positively associated with behavioral intentions. The study also found that perceived switching costs did not moderate the links between those variables, whereas perceived switching inducements moderated the links between banner advertising and perceived online security to online behavior intentions.
Newly trained lexical categories produce lateralized categorical perception of color

Linguistic categories have been shown to influence perceptual discrimination, to do so preferentially in the right visual field, to fail to do so when competing demands are made on verbal memory, and to vary with the color-term boundaries of different languages. However, because there are strong commonalities across languages in the placement of color-term boundaries, the question remains open whether observed categorical perception for color can be entirely a result of learned categories or may rely to some degree on innate ones. We show here that lateralized color categorical perception can be entirely the result of learned categories. In a visual search task, reaction times to targets were faster in the right than the left visual field when the target and distractor colors, initially sharing the same linguistic term (e.g., “blue”), became between-category colors after training (i.e., when two different shades of blue had each acquired a new name). A control group, whose conditions exactly matched those of the experimental group except that no new categories were introduced, did not show this effect, establishing that the effect was not dependent on increased familiarity with either the color stimuli or the task. The present results show beyond question that lateralized categorical perception of color can reflect strictly learned color categories, even artificially learned categories that violate both universal tendencies in color naming and the categorization pattern of the language of the subject.
University of Birmingham Optimisation of engineered Escherichia coli biofilms for enzymatic biosynthesis of l-halotryptophans

Engineered biofilms comprising a single recombinant species have demonstrated remarkable activity as novel biocatalysts for a range of applications. In this work, we focused on the biotransformation of 5-haloindole into 5-halotryptophan, a pharmaceutical intermediate, using Escherichia coli expressing a recombinant tryptophan synthase enzyme encoded by plasmid pSTB7. To optimise the reaction we compared two E. coli K-12 strains (MC4100 and MG1655) and their ompR234 mutants, which overproduce the adhesin curli (PHL644 and PHL628). The ompR234 mutation increased the quantity of biofilm in both MG1655 and MC4100 backgrounds. In all cases, no conversion of 5-haloindoles was observed using cells without the pSTB7 plasmid. Engineered biofilms of strains PHL628 pSTB7 and PHL644 pSTB7 generated more 5-halotryptophan than their corresponding planktonic cells. Flow cytometry revealed that the vast majority of cells were alive after 24 hour biotransformation reactions, both in planktonic and biofilm forms, suggesting that cell viability was not a major factor in the greater performance of biofilm reactions. Monitoring 5-haloindole depletion, 5-halotryptophan synthesis and the percentage conversion of the biotransformation reaction suggested that there were inherent differences between strains MG1655 and MC4100, and between planktonic and biofilm cells, in terms of tryptophan and indole metabolism and transport. The study has reinforced the need to thoroughly investigate bacterial physiology and make informed strain selections when developing biotransformation reactions.