Miracle-dz/UniFAR-FTUs huggingface dataset:
Biological Motion Shown Backwards: The Apparent-Facing Effect

We examined how showing a film backwards (reverse transformation) affects the visual perception of biological motion. Adults and 6-year-old children saw first a point-light quadruped moving normally as if on a treadmill, and then saw the same display in reverse transformation. For other groups the order of presentation was the opposite. Irrespective of the presentation mode (normal or reverse) and of the facing of the point-light figure (rightward or leftward), a pronounced apparent-facing effect was observed: the perceptual identification of a display was mainly determined by the apparent direction of locomotion. The findings suggest that in interpreting impoverished point-light biological-motion stimuli the visual system may neglect distortions caused by showing a film backwards. This property appears to be robust across perceptual development. Possible explanations of the apparent-facing effect are discussed.
Referral Pattern and Timing of Repair Are Risk Factors for Complications After Reconstructive Surgery for Bile Duct Injury

Background:The aim of the present study was to assess the role of the referral pattern and the timing of the surgical procedure on outcome after reconstructive surgery for bile duct injury (BDI). Summary Background Data:BDI after laparoscopic cholecystectomy remains a major problem in current surgical practice. Controversy exists about the influence of previous interventions before referral and the timing of repair on outcome. Methods:Of 500 patients referred to a tertiary center, 151 patients (30.2%) underwent reconstructive surgery for BDI. The influence of referral pattern was analyzed by defining patients as primary and secondary referred patients. The influence of timing of repair was investigated by categorizing 3 groups of patients: A, acute repair; B, delayed repair; and C, late repair. Results:Hospital mortality was zero. Perioperative complications occurred in 29 patients (19.2%): in 26.4% in secondary referred patients and 7.9% in primary referred patients (P = 0.04). Perioperative complications occurred in group A in 33.3%, in group B in 15.6%, and in group C in 22.5% (P = 0.22). Postoperative strictures occurred significantly more often in patients operated in the acute phase (P < 0.01) and in secondary referred patients (P = 0.03). A multivariate analysis identified 3 independent negative predictive factors for outcome: extended injury in the biliary tree (odds ratio = 3.70; confidence interval, 1.32–10.34), secondary referral (odds ratio = 4.35; confidence interval, 1.12–16.76), and repair in the acute phase after injury (odds ratio = 5.44; confidence interval, 1.2–24.43). Conclusions:Reconstructive surgery for the treatment of BDI is associated with acceptable morbidity and no mortality. Extended injury to the bile duct, referral to a tertiary center after therapeutic interventions, and acute repair are independent negative predictors on outcome after reconstructive surgery for BDI.
Prognostic factors of non-HIV immunocompromised patients with pulmonary infiltrates.

STUDY OBJECTIVES To assess the outcome and the prognostic factors in 200 non-HIV immunocompromised patients with pulmonary infiltrates (PIs). DESIGN Prospective observational study. SETTING An 800-bed university hospital. PATIENTS Two hundred non-HIV immunocompromised patients (hematologic malignancies, 79 patients; hematopoietic stem cell transplants [HSCTs], 61 patients; and solid-organ transplants, 60 patients). METHODS Investigation of prognostic factors related to mortality using a multiple logistic regression model. RESULTS Specific diagnosis of the PI was obtained in 78% of the cases (infectious origin was determined in 74%). The overall mortality rate was 39% (78 of 200 patients). Patients with HSCT had the highest mortality rate (53%). A requirement for mechanical ventilation (odds ratio [OR], 28; 95% confidence interval [CI], 9 to 93), an APACHE (acute physiology and chronic health evaluation) II score of > 20 (OR, 5.5; 95% CI, 2 to 14.7), and a delay of > 5 days in establishing a specific diagnosis (OR, 3.4; 95% CI, 1.2 to 9.6) were the variables associated with mortality at the multivariate analysis. The subgroup analysis based on underlying disease confirmed the prognostic significance of these variables and the infectious etiology for the PI. CONCLUSIONS Mortality in immunocompromised patients is high, particularly in patients undergoing HSCT. Achieving an earlier diagnosis potentially may improve the mortality rate of these patients.
Improved accuracy using recursive Bayesian estimation based language model fusion in ERP-based BCI typing systems

RSVP Keyboard™ is an electroencephalography (EEG) based brain computer interface (BCI) typing system, designed as an assistive technology for the communication needs of people with locked-in syndrome (LIS). It relies on rapid serial visual presentation (RSVP) and does not require precise eye gaze control. Existing BCI typing systems which uses event related potentials (ERP) in EEG suffer from low accuracy due to low signal-to-noise ratio. Henceforth, RSVP Keyboard™ utilizes a context based decision making via incorporating a language model, to improve the accuracy of letter decisions. To further improve the contributions of the language model, we propose recursive Bayesian estimation, which relies on non-committing string decisions, and conduct an offline analysis, which compares it with the existing naïve Bayesian fusion approach. The results indicate the superiority of the recursive Bayesian fusion and in the next generation of RSVP Keyboard™ we plan to incorporate this new approach.
A reciprocal peer review system to support college students' writing

As students' problem-solving processes in writing are rarely observed in face-to-face instruction, they have few opportunities to participate collaboratively in peer review to improve their texts. This study reports the design of a reciprocal peer review system for students to observe and learn from each other when writing. A sample of 95 undergraduate students was recruited to construct texts with the support of web-based reciprocal peer review in the processes of modelling, coaching, scaffolding, articulation, reflection and exploration. The results of the study revealed that these six processes helped students externalise and visualise their internal writing processes so that they could observe and learn from peers in writing as well as support peers in making text revisions. During their extensive and reciprocal interactions with various peers, students addressed mutual concerns in each other's text revisions. They constructed collaborative language knowledge for text improvement as local revisions (grammatical corrections) and global revisions (corrections on the development, organization or style of a text) were made in their final texts. The students' perceptions towards text improvement in this web-based peer review of modelling, coaching, scaffolding, articulation, reflection and exploration are also discussed in this study. [ABSTRACT FROM AUTHOR]
Cellular response in subretinal neovascularization induced by bFGF-impregnated microspheres.

PURPOSE To determine the sequence of cellular changes associated with a new rabbit model of subretinal neovascularization (SRN) induced by subretinal injection of basic fibroblast growth factor (bFGF)-impregnated microspheres. METHODS bFGF-impregnated gelatin microspheres, prepared by forming a polyion complex between gelatin and bFGF, were subretinally implanted into rabbit eyes. The eyes were studied by immunochemistry at 3 days to 8 weeks after implantation. Antibodies to CD4, CD8, cytokeratin, CD31, glial fibrillary acidic protein (GFAP), and RAM11 were used. RESULTS Cytokeratin-positive retinal pigment epithelial (RPE) cells appeared on day 3 and continued to increase in number in the subretinal space throughout the growth of the SRN membrane, becoming the predominant cell type. Macrophages (RAM11-positive) appeared early, but most disappeared within 7 days. GFAP-positive Müller cells were evident early in the retina but migrated into the subretinal space after 7 days; the gliotic adhesion they formed between the retina and the SRN membrane was prominent at 8 weeks. CD31-positive endothelial cells were first evident at 14 days and formed neovascular channels that were still present for up to 8 weeks. CD4- and CD8-positive lymphocytes appeared in the early stages but were few in number. CONCLUSIONS SRN membranes are primarily composed of RPE cells and vascular endothelial cells. The membrane adheres to the retina by a gliotic band. The cellular components involved in the membrane of this model resemble those found in SRN membranes removed from patients with age-related macular degeneration.
A Rapid Subcortical Amygdala Route for Faces Irrespective of Spatial Frequency and Emotion

There is significant controversy over the existence and function of a direct subcortical visual pathway to the amygdala. It is thought that this pathway rapidly transmits low spatial frequency information to the amygdala independently of the cortex, and yet the directionality of this function has never been determined. We used magnetoencephalography to measure neural activity while human participants discriminated the gender of neutral and fearful faces filtered for low or high spatial frequencies. We applied dynamic causal modeling to demonstrate that the most likely underlying neural network consisted of a pulvinar-amygdala connection that was uninfluenced by spatial frequency or emotion, and a cortical-amygdala connection that conveyed high spatial frequencies. Crucially, data-driven neural simulations revealed a clear temporal advantage of the subcortical connection over the cortical connection in influencing amygdala activity. Thus, our findings support the existence of a rapid subcortical pathway that is nonselective in terms of the spatial frequency or emotional content of faces. We propose that that the “coarseness” of the subcortical route may be better reframed as “generalized. ” SIGNIFICANCE STATEMENT The human amygdala coordinates how we respond to biologically relevant stimuli, such as threat or reward. It has been postulated that the amygdala first receives visual input via a rapid subcortical route that conveys “coarse” information, namely, low spatial frequencies. For the first time, the present paper provides direction-specific evidence from computational modeling that the subcortical route plays a generalized role in visual processing by rapidly transmitting raw, unfiltered information directly to the amygdala. This calls into question a widely held assumption across human and animal research that fear responses are produced faster by low spatial frequencies. Our proposed mechanism suggests organisms quickly generate fear responses to a wide range of visual properties, heavily implicating future research on anxiety-prevention strategies.
Handwriting Segmentation Contest

This paper presents the results of the handwriting segmentation contest that was organized in the context of ICDAR2007. The aim of this contest was to use well established evaluation practices and procedures in order to record recent advances in off-line handwriting segmentation. Two benchmarking datasets (one for text line and one for word segmentation) were used in a common evaluation platform in order to test and compare all submitted algorithms for handwritten document segmentation in realistic circumstances. The results of the evaluation of five algorithms submitted by participants as well as of two state-of-the-art algorithms are presented. The performance evaluation method is based on counting the number of matches between the text lines or words detected by the algorithms and the text line or words of the ground truth.
Expression of the Interleukin-7 Receptor Alpha Chain (CD127) on Virus-Specific CD8+ T Cells Identifies Functionally and Phenotypically Defined Memory T Cells during Acute Resolving Hepatitis B Virus Infection

ABSTRACT Virus-specific CD8+ T cells play a central role in the outcome of several viral infections, including hepatitis B virus (HBV) infection. A key feature of virus-specific CD8+ T cells is the development of memory. The mechanisms resulting in the establishment of T-cell memory are still only poorly understood. It has been suggested that T-cell memory may depend on the survival of virus-specific CD8+ T cells in the contraction phase. Indeed, a population of effector cells that express high levels of the interleukin-7 receptor alpha chain (CD127) as the precursors of memory CD8+ T cells has recently been identified in mice. However, very little information is currently available about the kinetics of CD127 expression in an acute resolving viral infection in humans and its association with disease pathogenesis, viral load, and functional and phenotypical T-cell characteristics. To address these important issues, we analyzed the HBV-specific CD8+ T-cell response longitudinally in a cohort of six patients with acute HBV infection who spontaneously cleared the virus. We observed the emergence of CD127 expression on antigen-specific CD8+ memory T cells during the course of infection. Importantly, the up-regulation of CD127 correlated phenotypically with a loss of CD38 and PD-1 expression and acquisition of CCR7 expression: functionally with an enhanced proliferative capacity and clinically with the decline in serum alanine aminotransferase levels and viral clearance. These results suggest that the expression of CD127 is a marker for the development of functionally and phenotypically defined antigen-specific CD8+ memory T cells in cleared human viral infections.
Longer Leukocyte Telomere Length Is Associated with Smaller Hippocampal Volume among Non-Demented APOE ε3/ε3 Subjects

Telomere length shortens with cellular division, and leukocyte telomere length is used as a marker for systemic telomere length. The hippocampus hosts adult neurogenesis and is an important structure for episodic memory, and carriers of the apolipoprotein E ε4 allele exhibit higher hippocampal atrophy rates and differing telomere dynamics compared with non-carriers. The authors investigated whether leukocyte telomere length was associated with hippocampal volume in 57 cognitively intact subjects (29 ε3/ε3 carriers; 28 ε4 carriers) aged 49–79 yr. Leukocyte telomere length correlated inversely with left (rs = −0.465; p = 0.011), right (rs = −0.414; p = 0.025), and total hippocampus volume (rs = −0.519; p = 0.004) among APOE ε3/ε3 carriers, but not among ε4 carriers. However, the ε4 carriers fit with the general correlation pattern exhibited by the ε3/ε3 carriers, as ε4 carriers on average had longer telomeres and smaller hippocampi compared with ε3/ε3 carriers. The relationship observed can be interpreted as long telomeres representing a history of relatively low cellular proliferation, reflected in smaller hippocampal volumes. The results support the potential of leukocyte telomere length being used as a biomarker for tapping functional and structural processes of the aging brain.
An analysis of the frequencies of finger tremor in healthy subjects

It has long been known that muscular activity even in healthy subjects is associated with tremor, but the reason for this association has not been clear. The present investigation was undertaken in the hope of throwing more light on the mechanisms determining tremor frequency. Since individual motor units are known to fire at frequencies below that necessary to produce a fused tetanus, one possibility is that tremor may represent the pattern of firing rates of the motor units. On this view, the normal smoothness of the myogram depends on the asynchronous discharge of different motor units and tremor is to be regarded as a partial failure in this asynchrony. When the tension exerted by the muscle is increased, the firing rates will also increase, particularly if the muscle is contracting minimally (Lindsley, 1935; Weddell, Feinstein & Pattle, 1944; Bigland & Lippold, 1954), and the tremor rate would be expected to alter accordingly. Many workers, however, following Schafer (1886), report a surprisingly constant tremor rate with a frequency of about 10 c/s. In the present experiments the frequency of tremor has been recorded in different subjects and at different strengths of muscular contraction and has been found to show little variation. This regular rhythm may arise in some part of the central nervous system above the anterior horn cell, as many workers have believed, but it is also possible that it is produced in the reflex arc. The stretch reflex, like other servomechanisms, may exhibit instability and oscillate at a particular frequency, related to the delay round the loop. If the period of oscillation in the muscle is twice as long as the delay round the loop, the negative feed-back will become positive because its phase is reversed by the delay round the loop, and in this case the oscillation may be self-maintained. (This is only strictly true of a servo with linear components, but will serve as an approximation.) The delay
Investigations on Word Senses and Word Usages

The vast majority of work on word senses has relied on predefined sense inventories and an annotation schema where each word instance is tagged with the best fitting sense. This paper examines the case for a graded notion of word meaning in two experiments, one which uses WordNet senses in a graded fashion, contrasted with the "winner takes all" annotation, and one which asks annotators to judge the similarity of two usages. We find that the graded responses correlate with annotations from previous datasets, but sense assignments are used in a way that weakens the case for clear cut sense boundaries. The responses from both experiments correlate with the overlap of paraphrases from the English lexical substitution task which bodes well for the use of substitutes as a proxy for word sense. This paper also provides two novel datasets which can be used for evaluating computational systems.
The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation

We show that the splicing regulator PTBP2 controls a genetic program essential for neuronal maturation. Depletion of PTBP2 in developing mouse cortex leads to degeneration of these tissues over the first three postnatal weeks, a time when the normal cortex expands and develops mature circuits. Cultured Ptbp2−/− neurons exhibit the same initial viability as wild type, with proper neurite outgrowth and marker expression. However, these mutant cells subsequently fail to mature and die after a week in culture. Transcriptome-wide analyses identify many exons that share a pattern of mis-regulation in the mutant brains, where isoforms normally found in adults are precociously expressed in the developing embryo. These transcripts encode proteins affecting neurite growth, pre- and post-synaptic assembly, and synaptic transmission. Our results define a new genetic regulatory program, where PTBP2 acts to temporarily repress expression of adult protein isoforms until the final maturation of the neuron. DOI: http://dx.doi. org/10.7554/eLife.01201. 001
Transcription, processing and function of CRISPR cassettes in Escherichia coli

CRISPR/Cas, bacterial and archaeal systems of interference with foreign genetic elements such as viruses or plasmids, consist of DNA loci called CRISPR cassettes (a set of variable spacers regularly separated by palindromic repeats) and associated cas genes. When a CRISPR spacer sequence exactly matches a sequence in a viral genome, the cell can become resistant to the virus. The CRISPR/Cas systems function through small RNAs originating from longer CRISPR cassette transcripts. While laboratory strains of Escherichia coli contain a functional CRISPR/Cas system (as judged by appearance of phage resistance at conditions of artificial co‐overexpression of Cas genes and a CRISPR cassette engineered to target a λ‐phage), no natural phage resistance due to CRISPR system function was observed in this best‐studied organism and no E. coli CRISPR spacer matches sequences of well‐studied E. coli phages. To better understand the apparently ‘silent’E. coli CRISPR/Cas system, we systematically characterized processed transcripts from CRISPR cassettes. Using an engineered strain with genomically located spacer matching phage λ we show that endogenous levels of CRISPR cassette and cas genes expression allow only weak protection against infection with the phage. However, derepression of the CRISPR/Cas system by disruption of the hns gene leads to high level of protection.
The Multifaceted Proteins MvaT and MvaU, Members of the H-NS Family, Control Arginine Metabolism, Pyocyanin Synthesis, and Prophage Activation in Pseudomonas aeruginosa PAO1

ABSTRACT The MvaT and MvaU proteins belonging to the H-NS family were identified as DNA-binding proteins that interact with the regulatory region of the aotJQMOP-argR operon for arginine uptake and regulation. Recombinant MvaT and MvaU proteins were purified, and binding of these purified proteins to the aotJ regulatory region was demonstrated using electromobility shift assays. Polyclonal antibodies against purified MvaT and MvaU were prepared and employed in supershift assays to support these observations. Knockout mutations resulting in a single lesion in mvaT or mvaU, as well as knockout mutations resulting in double lesions, were constructed using biparental conjugation, and the absence of MvaT and MvaU in the resulting mutants was confirmed by immunoblot analysis. Using measurements of the β-galactosidase activities from aotJ::lacZ fusions in the mutants and the parental strain, it was found that MvaT and MvaU serve as repressors in control of aotJ expression. The effects of MvaT and MvaU on pyocyanin synthesis and CupA fimbrial expression in these mutants were also analyzed. Pyocyanin synthesis was induced in the single mutants but was completely abolished in the double mutant, suggesting that there is a complicated regulatory scheme in which MvaT and MvaU are essential elements. In comparison, MvaT had a more profound role than MvaU as a repressor of cupA expression; however, a combination of MvaT depletion and MvaU depletion had a strong synergistic effect on cupA. Moreover, prophage Pf4 integrated into the chromosome of Pseudomonas aeruginosa PAO1 was activated in an mvaT mvaU double mutant but not in a single mutant. These results were supported by purification and nucleotide sequencing of replicative-form DNA and by the release of phage particles in plaque assays. In summary, the mvaT mvaU double mutant was viable, and depletion of MvaT and MvaU had serious effects on a variety of physiological functions in P. aeruginosa.
Changes in Levels of Dopamine and Tyramine in the Rat Caudate Nucleus Following Alterations of Impulse Flow in the Nigrostriatal Pathway

Abstract: Following electrical stimulation of the substantia nigra for 1 h there was a substantial increase in dopamine (DA) turnover in the rat caudate nucleus evidenced by an increase in its acid metabolite homovanillic acid (HVA). Concurrently there was an increase in striatal m‐tyramine (mTA) and a substantial decrease in p‐tyramine (pTA). Lesioning the substantia nigra to decrease impulse flow resulted in a buildup of striatal DA and mTA, but again a decrease in pTA. Following pre‐treatment with a tyrosine hydroxylase inhibitor, the effects of stimulation of the nigra on mTA were reversed, there being a significant decrease in this amine. The decrease of pTA in response was partially prevented by tyrosine hydroxylase inhibition. The effects of stimulation or substantia nigra lesions on pTA levels were reversed, however, by tyrosine hydroxylase inhibition, a significant increase in this amine being recorded. mTA and DA levels were largely unaffected by a combination of lesion and tyrosine hydroxylase inhibition. The results provide insight into the possible biosynthetic interrelationships between DA and the tyramine isomers in the rat caudate nucleus.