Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of microtubule dynamics and nucleation during polarization in MDCK II cells

MDCK cells form a polarized epithelium when they reach confluence in tissue culture. We have previously shown that concomitantly with the establishment of intercellular junctions, centrioles separate and microtubules lose their radial organization (Bacallao, R., C. Antony, C. Dotti, E. Karsenti, E.H.K. Stelzer, and K. Simons. 1989. J. Cell Biol. 109:2817-2832. Buendia, B., M.H. Bre, G. Griffiths, and E. Karsenti. 1990. 110:1123-1136). In this work, we have examined the pattern of microtubule nucleation before and after the establishment of intercellular contacts. We analyzed the elongation rate and stability of microtubules in single and confluent cells. This was achieved by microinjection of Paramecium axonemal tubulin and detection of the newly incorporated subunits by an antibody directed specifically against the Paramecium axonemal tubulin. The determination of newly nucleated microtubule localization has been made possible by the use of advanced double-immunofluorescence confocal microscopy. We have shown that in single cells, newly nucleated microtubules originate from several sites concentrated in a region localized close to the nucleus and not from a single spot that could correspond to a pair of centrioles. In confluent cells, newly nucleated microtubules were still more dispersed. The microtubule elongation rate of individual microtubules was not different in single and confluent cells (4 microns/min). However, in confluent cells, the population of long lived microtubules was strongly increased. In single or subconfluent cells most microtubules showed a t1/2 of less than 30 min, whereas in confluent monolayers, a large population of microtubules had a t1/2 of greater than 2 h. These results, together with previous observations cited above, indicate that during the establishment of polarity in MDCK cells, microtubule reorganization involves both a relocalization of microtubule-nucleating activity and increased microtubule stabilization.
Adverse drug events in hospitalized patients. Excess length of stay, extra costs, and attributable mortality.

OBJECTIVE To determine the excess length of stay, extra costs, and mortality attributable to adverse drug events (ADEs) in hospitalized patients. DESIGN Matched case-control study. SETTING The LDS Hospital, a tertiary care health care institution. PATIENTS All patients admitted to LDS Hospital from January 1, 1990, to December 31, 1993, were eligible. Cases were defined as patients with ADEs that occurred during hospitalization; controls were selected according to matching variables in a stepwise fashion. METHODS Controls were matched to cases on primary discharge diagnosis related group (DRG), age, sex, acuity, and year of admission; varying numbers of controls were matched to each case. Matching was successful for 71% of the cases, leading to 1580 cases and 20,197 controls. MAIN OUTCOME MEASURES Crude and attributable mortality, crude and attributable length of stay, and cost of hospitalization. RESULTS ADEs complicated 2.43 per 100 admissions to the LDS Hospital during the study period. The crude mortality rates for the cases and matched controls were 3.5% and 1.05%, respectively (P<.001). The mean length of hospital stay significantly differed between the cases and matched controls (7.69 vs 4.46 days; P<.001) as did the mean cost of hospitalization ($10,010 vs $5355; P<.001). The extra length of hospital stay attributable to an ADE was 1.74 days (P<.001). The excess cost of hospitalization attributable to an ADE was $2013 (P<.001). A linear regression analysis for length of stay and cost controlling for all matching variables revealed that the occurrence of an ADE was associated with increased length of stay of 1.91 days and an increased cost of $2262 (P<.001). In a similar logistic regression analysis for mortality, the increased risk of death among patients experiencing an ADE was 1.88 (95% confidence interval, 1.54-2.22; P<.001). CONCLUSION The attributable lengths of stay and costs of hospitalization for ADEs are substantial. An ADE is associated with a significantly prolonged length of stay, increased economic burden, and an almost 2-fold increased risk of death.
Demonstration of Joshua: An Open Source Toolkit for Parsing-based Machine Translation

We describe Joshua, an open source toolkit for statistical machine translation. Joshua implements all of the algorithms required for synchronous context free grammars (SCFGs): chart-parsing, n-gram language model integration, beam-and cube-pruning, and k-best extraction. The toolkit also implements suffix-array grammar extraction and minimum error rate training. It uses parallel and distributed computing techniques for scalability. We demonstrate that the toolkit achieves state of the art translation performance on the WMT09 French-English translation task.
Finger Numeral Representations: More than Just Another Symbolic Code

Representing numerosities with finger configurations offers children the opportunity to learn and internalize fundamental properties of natural numbers through sensory–motor interactions with the world. Recent findings show that even educated adults use their fingers as a visuo-motor support to process, represent, and communicate numerosities. Indeed, using fingers to represent numerosities prototypically has been shown to give the corresponding finger configurations a special status in long-term memory: these configurations are recognized and processed faster than other finger configurations, providing a direct access to number magnitude, what other finger configurations do less efficiently. This occurs for configurations stemming from finger counting (i.e., the way the fingers are raised to count for oneself; for example, thumb, index, and middle fingers for numerosity {3}) and from finger montring (i.e., the way fingers are raised to show numerosities to someone else; for example, index, middle, and ring fingers for numerosity {3}). However, finger numeral representation is not just another way of representing numerical magnitudes mentally. We argue that it also contributes to acquiring, building, and then accessing number semantics, and that, compared to other numerical representations, it provides an extra value by rooting number meaning in a culturally shared yet non-arbitrary and self-experienced sensory–motor representation.
Annotated Bibliography : Factors in College Retention and Persistence October , 2013 Prepared by Kate Ford , Center for Innovation in Learning

This conceptual path model of the dropout process, developed prior to proliferation of online learning, defined non-traditional students as older (age 25 or over), part-time commuter students, a population overlooked by previous social integration models of student retention proffered by Spady (1970) Tinto (1975), and Pascarella (1980). The authors built on the previous models, retaining the background and academic integration variables expected to impact retention for non-traditional students. Their model addressed the greater impact of the external environment on the non-traditional student. The variables in the model were chosen for their predictive ability and include academic performance, intent to leave, high school GPA, college goals, and environmental factors. Linkages between the variables were based on behavioral theories and the previous models of student attrition.
Is there a smarter way to use 100 billion transistors?

Within the next decade it will be possible to build chip multiprocessors with thousands of cores. We can expect such devices to be exceptionally good at the kinds of problems massively parallel computers are already good at. That leaves a large class of interesting problems, especially those of artificial intelligence, for which multi-core processors are less well suited. Are there alternative architectures, scalable to 100 billion transistors and beyond, tolerant to device faults and process variations, and more appropriate for artificial intelligence problems than thousands of cores connected by a network on chip?
Fertility in Hypophysectomized Pituitary Grafting: Part i Function and·

Male rats underwent hypophysectomy and graft procedures, and a normal control group (C) was also established. In the hypophysectomy-plus-pituitary graft (HC) group, a suspension of neonatal rat pituitary cells (cortical ce lls in the hypophysectomy-plus-cortical graft (CC) group) was implanted into the third ventride. Four weeks later, the surviving hypophysectomy only H (n=21), HC (n=21), and CC (n=21) rats were evaluated for copulation/ ejaculation/ fertility. Endocrine target organs were histologically examined, and serum levels of luteinising hormone (LH) and testosterone were compared among the four groups. LH response to endogenous (cold stress) and exogenous (gonadotropin-releasing hormone injection) stimuli was also assessed in the experimental groups. The HC group had higher LH than the H and CC groups (0.89 ± 0.2 pg/ml versus 0.58 ± 0.2 pg/ml and 0.47 ± 0.3 pg/ml, respectively; p<0.05), but lower LH than controls (p<0.05). The LH response to exogenous and endogenous stimuli was greater in the HC than in the H and CC rats (p<0.05). Only control rats had detectable testosterone. HC rats (52.4%) were more sexuallyactive than H (5.3%) and CC (5.5%) animals (p<O.OO1). Histologically, grade 3 thyroidal and testicular atrophy predominated in the H and CC groups (17 (89.5%) and 15 (83.3%) rats, respectively), whereas grade 2 atrophy predominated in the HC animals (17 (81 %)). Implantation of neonatal pituitary grafts into the third ventride of hypophysectomized rats caused LH secretion to rise, but not enough to stimulate testosterone secretion.
Disambiguating Between Generic and Referential “You” in Dialog

We describe an algorithm for a novel task: disambiguating the pronoun you in conversation. You can be generic or referential; finding referential you is important for tasks such as addressee identification or extracting 'owners' of action items. Our classifier achieves 84% accuracy in two-person conversations; an initial study shows promising performance even on more complex multi-party meetings.
Replication Fork Reversal Occurs Spontaneously after Digestion but Is Constrained in Supercoiled Domains*

Replication fork reversal was investigated in undigested and linearized replication intermediates of bacterial DNA plasmids containing a stalled fork. Two-dimensional agarose gel electrophoresis, a branch migration and extrusion assay, electron microscopy, and DNA-psoralen cross-linking were used to show that extensive replication fork reversal and extrusion of the nascent-nascent duplex occurs spontaneously after DNA nicking and restriction enzyme digestion but that fork retreat is severely limited in covalently closed supercoiled domains.
MYC, Metabolism, and Cancer.

UNLABELLED The MYC oncogene encodes a transcription factor, MYC, whose broad effects make its precise oncogenic role enigmatically elusive. The evidence to date suggests that MYC triggers selective gene expression amplification to promote cell growth and proliferation. Through its targets, MYC coordinates nutrient acquisition to produce ATP and key cellular building blocks that increase cell mass and trigger DNA replication and cell division. In cancer, genetic and epigenetic derangements silence checkpoints and unleash MYC's cell growth- and proliferation-promoting metabolic activities. Unbridled growth in response to deregulated MYC expression creates dependence on MYC-driven metabolic pathways, such that reliance on specific metabolic enzymes provides novel targets for cancer therapy. SIGNIFICANCE MYC's expression and activity are tightly regulated in normal cells by multiple mechanisms, including a dependence upon growth factor stimulation and replete nutrient status. In cancer, genetic deregulation of MYC expression and loss of checkpoint components, such as TP53, permit MYC to drive malignant transformation. However, because of the reliance of MYC-driven cancers on specific metabolic pathways, synthetic lethal interactions between MYC overexpression and specific enzyme inhibitors provide novel cancer therapeutic opportunities.
Treatment of presumed hypotension in very low birthweight neonates: effects on regional cerebral oxygenation

Context Previous studies have correlated poor neurological outcomes with hypotension. Treatment of hypotension in very low birthweight (VLBW) infants is common, and most often is based solely on the blood pressure measurement. Whether treatment improves cerebral oxygenation is unclear. Objective To determine if treatment of hypotension in VLBW neonates results in an increase in cerebral oxygenation. Patients and methods In this single centre observational study, neonates <30 weeks and <1500 grams, blood pressure and regional cerebral oximetry (rCSO2) with near infrared spectroscopy were continuously monitored and digitally recorded. If patients were treated for hypotension during the first 3 days of life, effects of treatment on blood pressure and regional cerebral saturation were determined. Results Twenty-eight of 50 patients were treated by the medical team for hypotension, of which 22 had accurate data recorded for analysis. Both normal saline 10 ml/kg, and dopamine 2.5–5 mcg/kg per min significantly increased blood pressure, (saline 26.8±3.5 to 28.8±4.2 mm Hg, p<0.005; dopamine 27.6±1.9 to 29.5±3.2 mm Hg, p<0.02). Pre-treatment values of rCSO2 were similar to published normative values and treatment with either normal saline or dopamine had no effect on rCSO2. Conclusion These results suggest that treating hypotension in VLBW neonates based solely on a blood pressure measurement of less than 30 mm Hg, while increasing blood pressure, may not increase cerebral oxygenation, possibly because many of these patients are in the autoregulatory zone for cerebral blood flow.
Animal Models of Periventricular Leukomalacia

Periventricular leukomalacia, specifically characterized as white matter injury, in neonates is strongly associated with the damage of pre-myelinating oligodendrocytes. Clinical data suggest that hypoxia-ischemia during delivery and intrauterine or neonatal infection-inflammation are important factors in the etiology of periventricular leukomalacia including cerebral palsy, a serious case exhibiting neurobehavioral deficits of periventricular leukomalacia. In order to explore the pathophysiological mechanisms of white matter injury and to better understand how infectious agents may affect the vulnerability of the immature brain to injury, novel animal models have been developed using hypoperfusion, microbes or bacterial products (lipopolysaccharide) and excitotoxins. Such efforts have developed rat models that produce predominantly white matter lesions by adopting combined hypoxia-ischemia technique on postnatal days 1-7, in which unilateral or bilateral carotid arteries of animals are occluded (ischemia) followed by 1-2 hour exposure to 6-8% oxygen environment (hypoxia). Furthermore, low doses of lipopolysaccharide that by themselves have no adverse-effects in 7-day-old rats, dramatically increase brain injury to hypoxic-ischemic challenge, implying that inflammation sensitizes the immature central nervous system. Therefore, among numerous models of periventricular leukomalacia, combination of hypoxia-ischemia-lipopolysaccharide might be one of the most-acceptable rodent models to induce extensive white matter injury and ensuing neurobehavioral deficits for the evaluation of candidate therapeutics.
Masking by ipsilateral and contralateral maskers.

Contralateral masking occurs when the threshold of a signal in one ear is elevated by the presence of a masker in the other, contralateral ear. The classic data and theory on contralateral masking were provided by Zwislocki [J. Acoust. Soc. Am. 52, 644-659 (1972)] who observed a 3- to 18-dB threshold shift (masking) for a gated pure-tone signal in one ear when a gated pure-tone masker was presented via insert earphones to the other ear. Zwislocki referred to this phenomenon as "central masking. " Here, using two psychophysical methods (Yes-No; two-interval forced-choice), Zwislocki's original results, obtained with other psychophysical methods, were successfully replicated. Similar results using several psychophysical methods suggest that contralateral masking is indicative of a sensory phenomenon rather than observer bias and other response proclivities. In a second experiment, psychophysical tuning curves were obtained using either an ipsilateral masker or a contralateral masker. Tuning curves obtained with a contralateral masker had steeper slopes on both the low- and high-frequency sides than tuning curves obtained with an ipsilateral masker. Thus, although substantially smaller in effect than ipsilateral masking, contralateral masking is more sharply tuned. The sharp tuning of contralateral masking reflects a greater compression of the input/output functions for contralateral masking than for ipsilateral masking. The closest correspondence between the tuning curves reported here for contralateral masking and those predicted by Zwislocki's theory and data (on central masking) occurred for tuning curves where the ratio of driven activity to spontaneous activity was about six. A remaining issue is the role, if any, of the efferent auditory system, especially the olivocochlear bundle, in threshold shifts measured using the Zwislocki (central masking) paradigm.
Functional Centering

Based on empirical evidence from a free word order language (German) we propose a fundamental revision of the principles guiding the ordering of discourse entities in the forward-looking centers within the centering model. We claim that grammatical role criteria should be replaced by indicators of the functional information structure of the utterances, i.e., the distinction between context-bound and unbound discourse elements. This claim is backed up by an empirical evaluation of functional centering.
Job Loss, Unemployment and the Incidence of Hazardous Drinking during the Late 2000s Recession in Europe among Adults Aged 50–64 Years

Background To estimate the incidence of hazardous drinking in middle-aged people during an economic recession and ascertain whether individual job loss and contextual changes in unemployment influence the incidence rate in that period. Methods Longitudinal study based on two waves of the SHARE project (Survey of Health, Ageing and Retirement in Europe). Individuals aged 50–64 years from 11 European countries, who were not hazardous drinkers at baseline (n = 7,615), were selected for this study. We estimated the cumulative incidence of hazardous drinking (≥40g and ≥20g of pure alcohol on average in men and women, respectively) between 2006 and 2012. Furthermore, in the statistical analysis, multilevel Poisson regression models with robust variance were fitted and obtained Risk Ratios (RR) and their 95% Confidence Intervals (95%CI). Results Over a 6-year period, 505 subjects became hazardous drinkers, with cumulative incidence of 6.6 per 100 persons between 2006 and 2012 (95%CI:6.1–7.2). Age [RR = 1.02 (95%CI:1.00–1.04)] and becoming unemployed [RR = 1.55 (95%CI:1.08–2.23)] were independently associated with higher risk of becoming a hazardous drinker. Conversely, having poorer self-perceived health was associated with lower risk of becoming a hazardous drinker [RR = 0.75 (95%CI:0.60–0.95)]. At country-level, an increase in the unemployment rate during the study period [RR = 1.32 (95%CI:1.17–1.50)] and greater increases in the household disposable income [RR = 0.97 (95%CI:0.95–0.99)] were associated with risk of becoming a hazardous drinker. Conclusions Job loss among middle-aged individuals during the economic recession was positively associated with becoming a hazardous drinker. Changes in country-level variables were also related to this drinking pattern.
Rotavirus genotypes in children in the Basque Country (North of Spain): rapid and intense emergence of the G12[P8] genotype

SUMMARY Between July 2009 and June 2011, rotavirus was detected in 507 of 4597 episodes of acute gastroenteritis in children aged <3 years in Gipuzkoa (Basque Country, Spain), of which the G-type was determined in 458 (90·3%). During the annual seasonal epidemic of 2010–2011, the unusual G-type 12 was predominant, causing 65% (145/223) of cases of rotavirus gastroenteritis. All the G12 strains were clustered in lineage III and were preferentially associated with P-type 8. This epidemic was characterized by broad geographical distribution (rural and urban) and, over 7 months, affected both infants and children, the most frequently affected being children between 4 and 24 months. Of children with rotavirus G12, 16% required hospital admission, the admission rate in children aged <2 years being 20·7 cases/10 000 children. The sudden emergence and predominance of G12 rotaviruses documented in this winter outbreak suggest that they may soon become a major human rotavirus genotype.
Estimating Watermarking Capacity in Gray Scale Images Based on Image Complexity

Capacity is one of the most important parameters in image watermarking. Different works have been done on this subject with different assumptions on image and communication channel. However, there is not a global agreement to estimate watermarking capacity. In this paper, we suggest a method to find the capacity of images based on their complexities. We propose a new method to estimate image complexity based on the concept of Region Of Interest (ROI). Our experiments on 2000 images showed that the proposed measure has the best adoption with watermarking capacity in comparison with other complexity measures. In addition, we propose a new method to calculate capacity using proposed image complexity measure. Our proposed capacity estimation method shows better robustness and image quality in comparison with recent works in this field.
Stem Cell Repor ts

SUMMARY Lymphoid-primed multipotent progenitor (LMPP)-like and granulocyte-monocyte progenitor (GMP)-like leukemia stem cells (LSCs) co-exist in the blood of most patients with acute myeloid leukemia (AML). Complete elimination of both types of LSCs is required to cure AML. Using an MLL-AF9 -induced murine AML model, we studied the role of hematopoietic cytokines in the survival of LMPP-and GMP-like LSCs. We found that SCF or FLT3L promotes the survival of LMPP-like LSCs by stimulating Stat5-mediated Mcl1 expression, whereas interleukin-3 (IL-3) or IL-6 induces the survival of GMP-like LSCs by stimulating Stat3/nuclear factor k B (NF-k B)-mediated Bcl2 expression. Functional study demonstrated that, compared to AML cells cultured in IL-3 and IL-6 medium, AML cells in SCF-or Flt3L-only culture are highly clonogenic in in vitro culture and are highly leukemogenic in vivo . Our study suggests that co-inhibition of both STAT5-MCL1 and STAT3/NF-k B-BCL2 signaling might represent an improved treatment strategy against AML, speciﬁcally AML cases with a monocytic phenotype and/or FLT3 mutations.