Miracle-dz/UniFAR-FTUs huggingface dataset:
You Could Have Just Asked

In an earlier article (Galak & Meyvis, 2011), we reported eight studies that demonstrate people’s tendency to remember unpleasant experiences as more aversive when they think they will experience them again. Based on a test that, ironically, suffers from publication bias, Francis (2012) estimated that there is a high probability that we obtained at least one unsuccessful study that was left in the file drawer. He then argues that, because of this, our findings should be discounted. We propose that, instead of engaging in a statistical fishing expedition, Francis should have simply asked us for our file drawer. If he had done so, he would have quickly realized that a meta-analysis of all our studies (both published and unpublished) shows that the effect we reported is highly reliable. We suggest that when the answer is out there, it makes more sense to ask for it than to estimate it.
Physical descriptions of the bacterial nucleoid at large scales, and their biological implications

Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex and dynamic protein-rich state, which is highly organized at various length scales. This has implications for modulating (when not directly enabling) the core biological processes of replication, transcription and segregation. We overview the progress in this area, driven in the last few years by new scientific ideas and new interdisciplinary experimental techniques, ranging from high space- and time-resolution microscopy to high-throughput genomics employing sequencing to map different aspects of the nucleoid-related interactome. The aim of this review is to present the wide spectrum of experimental and theoretical findings coherently, from a physics viewpoint. In particular, we highlight the role that statistical and soft condensed matter physics play in describing this system of fundamental biological importance, specifically reviewing classic and more modern tools from the theory of polymers. We also discuss some attempts toward unifying interpretations of the current results, pointing to possible directions for future investigation.
Dealing with the Grey Sheep of the Romanian Gender System, the Neuter

Romanian has been traditionally seen as bearing three lexical genders: masculine, feminine, and neuter, although it has always been known to have only two agreement patterns (for masculine and feminine). Previous machine learning classifiers which have attempted to discriminate Romanian nouns according to gender have taken as input only the singular form, either presupposing the traditional tripartite analysis, or using additional information from case inflected forms. We present here a tool based on two parallel support vector machines using n-gram features from the singular and from the plural, which distinguish the neuter.
Pyruvate shuttling during rest and exercise before and after endurance training in men.

We describe the isotopic exchange of lactate and pyruvate after arm vein infusion of [3-(13)C]lactate in men during rest and exercise. We tested the hypothesis that working muscle (limb net lactate and pyruvate exchange) is the source of the elevated systemic lactate-to-pyruvate concentration ratio (L/P) during exercise. We also hypothesized that the isotopic equilibration between lactate and pyruvate would decrease in arterial blood as glycolytic flux, as determined by relative exercise intensity, increased. Nine men were studied at rest and during exercise before and after 9 wk of endurance training. Although during exercise arterial pyruvate concentration decreased to below rest values (P < 0.05), pyruvate net release from working muscle was as large as lactate net release under all exercise conditions. Exogenous (arterial) lactate was the predominant origin of pyruvate released from working muscle. With no significant effect of exercise intensity or training, arterial isotopic equilibration [(IE(pyruvate)/IE(lactate)). 100%, where IE is isotopic enrichment] decreased significantly (P < 0.05) from 60 +/- 3.1% at rest to an average value of 12 +/- 2.7% during exercise, and there were no changes in femoral venous isotopic equilibration. These data show that 1). the isotopic equilibration between lactate and pyruvate in arterial blood decreases significantly during exercise; 2). working muscle is not solely responsible for the decreased arterial isotopic equilibration or elevated arterial L/P occurring during exercise; 3). working muscle releases similar amounts of lactate and pyruvate, the predominant source of the latter being arterial lactate; 4). pyruvate clearance from blood occurs extensively outside of working muscle; and 5). working muscle also releases alanine, but alanine release is an order of magnitude smaller than lactate or pyruvate release. These results portray the complexity of metabolic integration among diverse tissue beds in vivo.
Autofluorescence spectroscopy of rat liver during experimental transplantation procedure. An approach for hepatic metabolism assessment

Ischemia–reperfusion injury, a major cause of organ metabolic alterations and consequent dysfunction in liver transplantation, could be overcome by optimizing organ preservation procedures. The potential of autofluorescence analysis was investigated with the aim to define parameters suitable for in vivo monitoring tissue functionality. Spectrofluorometric analysis was performed on explanted rat livers during cold storage, under standard (4 ◦C University of Wisconsin medium for 20 h) and purposely damaging (4 ◦C Eurocollins medium for 20, 43 and 72 h) preservation conditions, and reperfusion (rewarming–reoxygenation). For both preservation conditions, cold hypoxia caused a signal amplitude increase, mainly attributable to NAD(P)H, and a spectral shape modification, ascribable to changes in the relative contributions of NAD(P)H and flavins, as a result of the tissue reduced state enhancement. Upon rewarming–reoxygenation the autofluorescence signal decreased with a rate depending on the preservation conditions. The time constant changed according to the extent of the liver functionality impairment, as assessed by conventional biochemical and histochemical analyses, thus providing a parameter exploitable for an in situ , real time monitoring of the efficacy of experimental preservation procedures.
A Bayesian Approach to Modeling Associations Between Pulsatile Hormones

Summary Many hormones are secreted in pulses. The pulsatile relationship between hormones regulates many biological processes. To understand endocrine system regulation, time series of hormone concentrations are collected. The goal is to characterize pulsatile patterns and associations between hormones. Currently each hormone on each subject is fitted univariately. This leads to estimates of the number of pulses and estimates of the amount of hormone secreted; however, when the signal‐to‐noise ratio is small, pulse detection and parameter estimation remains difficult with existing approaches. In this article, we present a bivariate deconvolution model of pulsatile hormone data focusing on incorporating pulsatile associations. Through simulation, we exhibit that using the underlying pulsatile association between two hormones improves the estimation of the number of pulses and the other parameters defining each hormone. We develop the one‐to‐one, driver–response case and show how birth–death Markov chain Monte Carlo can be used for estimation. We exhibit these features through a simulation study and apply the method to luteinizing and follicle stimulating hormones.
Haemophilus influenzae type b lipooligosaccharide: stability of expression and association with virulence

Spontaneous antigenic and phenotypic variations in the lipooligosaccharide (LOS) of two strains of Haemophilus influenzae type b (Hib) were previously shown to be associated with changes in virulence (A. Kimura and E.J. Hansen, Infect. Immun. 51:69-79, 1986). The goal of the present study was to define further the stability of LOS expression by this pathogen and the role of Hib LOS in virulence. Variation in LOS antigenic reactivity, as detected with LOS-specific monoclonal antibodies, was observed in 3 of 30 Hib strains after single-colony passage. When large numbers of individual colonies from seven other Hib strains were screened, however, spontaneous LOS antigenic variation was detected in all of the strains. Antigenic variation was not consistently associated with an altered LOS phenotype, as determined by sodium dodecyl sulfate-polyacrylamide gradient gel electrophoresis and silver staining of LOS preparations. Changes in the LOS antigenic phenotype were correlated with altered virulence potential in two strains. In these strains, acquisition of reactivity with certain LOS-directed monoclonal antibodies was associated with the synthesis of a higher-molecular-weight LOS, enhanced virulence, and increased resistance to serum killing involving the classical complement pathway.
Glioblastoma Patients Epidermal Growth Factor Receptor , and Survival in Analysis of Complex Relationships between Age , p 53 , Updated

Glioblastoma multiforme (GBM) carries a dismal prognosis. However, a range of survival times exists, and parameters that define prognostic groups may help to optimize treatment. To identify such prognostic groups, we analyzed tumor tissue from 110 cases of newly diagnosed GBM from two clinical protocols. Similar to other studies, we found no association of epidermal growth factor receptor (EGFR) overexpression (as assessed by immunohistochemistry), p53 immunopositivity, or p53 mutation with survival in the entire sample. However, EGFR overexpression showed trends toward worse prognosis in patients younger than the median age, but better prognosis in patients older than the median age. This interaction of EGFR with age group was statistically significant and led us to focus our further analyses on the younger patients. In this group, a statistically significant association of EGFR overexpression with worse survival was identified in the p53-negative but not p53-positive tumors. We found a similar result after screening these cases for mutations in p53: EGFR overexpression was negatively associated with survival only in the p53 wild-type cases. To confirm this unexpected result, this finding was reproduced in a validation sample of an additional 42 tumors from younger patients on the same two clinical protocols. This complex relationship between EGFR and p53 in younger patients remained in a multivariate analysis that incorporated additional prognostic variables. The results suggest that analysis of prognostic markers in GBM is complex, and maximal information may require analysis of subgroups based on age and the status of specific markers such as p53. In addition, they suggest a specific group of patients on which to focus promising therapies targeting EGFR.
Differential NtcA Responsiveness to 2-Oxoglutarate Underlies the Diversity of C/N Balance Regulation in Prochlorococcus

Previous studies showed differences in the regulatory response to C/N balance in Prochlorococcus with respect to other cyanobacteria, but no information was available about its causes, or the ecological advantages conferred to thrive in oligotrophic environments. We addressed the changes in key enzymes (glutamine synthetase, isocitrate dehydrogenase) and the ntcA gene (the global nitrogen regulator) involved in C/N metabolism and its regulation, in three model Prochlorococcus strains: MED4, SS120, and MIT9313. We observed a remarkable level of diversity in their response to azaserine, a glutamate synthase inhibitor which increases the concentration of the key metabolite 2-oxoglutarate, used to sense the C/N balance by cyanobacteria. Besides, we studied the binding between the global nitrogen regulator (NtcA) and the promoter of the glnA gene in the same Prochlorococcus strains, and its dependence on the 2-oxoglutarate concentration, by using isothermal titration calorimetry, surface plasmon resonance, and electrophoretic mobility shift. Our results show a reduction in the responsiveness of NtcA to 2-oxoglutarate in Prochlorococcus, especially in the MED4 and SS120 strains. This suggests a trend to streamline the regulation of C/N metabolism in late-branching Prochlorococcus strains (MED4 and SS120), in adaptation to the rather stable conditions found in the oligotrophic ocean gyres where this microorganism is most abundant.
Characterization and Dynamic Behavior of Wild Yeast during Spontaneous Wine Fermentation in Steel Tanks and Amphorae

We studied the dynamic behavior of wild yeasts during spontaneous wine fermentation at a winery in the Valais region of Switzerland. Wild yeasts in the winery environment were characterized using a PCR-RFLP method. Up to 11 different yeast species were isolated from the vineyard air, whereas only seven were recovered from the grapes surface. We initially investigated a cultureindependent method in pilot-scale steel fermentation tanks and found a greater diversity of yeasts in the musts from two red grape varieties compared to three white grape varieties. We found that the yeasts Metschnikowia pulcherrima, Rhodotorula mucilaginosa, Pichia kluyveri, P. membranifaciens and Saccharomyces cerevisiae remained active at the end of the fermentation. We also studied the dynamic behavior of yeasts in Qvevris for the first time using a novel, highlysensitive quantitative real-time PCR method. We found that non-Saccharomyces yeasts were present during the entire fermentation process, with R. mucilaginosa and P. anomala the most prominent species. We studied the relationship between the predominance of different species and the output of the fermentation process. We identified so-called spoilage yeasts in all the fermentations, but high levels of acetic acid accumulated only in those fermentations with an extended lag phase.
Prognostic role of KRAS, NRAS, BRAF and PIK3CA mutations in advanced colorectal cancer.

AIM To explore the prognostic value of extended mutational profiling for metastatic colorectal cancer (mCRC). MATERIALS & METHODS We retrospectively reviewed survival results of 194 mCRC patients that were assigned to four molecular subgroups: BRAF mutated; KRAS mutated codons 12-13 only; any of KRAS codons 61-146, PIK3CA or NRAS mutations and all wild-type. Point mutations were investigated by pyrosequencing. RESULTS BRAF (5.2%) and KRAS 12-13 (31.9%) mutations were associated with poorer survival (HR 2.8 and 1.76, respectively). Presenting with right-sided colon cancer, not resected primary tumor, WBC >10 × 10(9)/l, receiving less chemotherapy or no bevacizumab were all associated with inferior outcome. The all-wild-type subgroup (39.2%) reported the longest survival. CONCLUSION Extended mutational profile combined with clinical factors may impact on survival in mCRC.
The Smallest Capsid Protein Mediates Binding of the Essential Tegument Protein pp150 to Stabilize DNA-Containing Capsids in Human Cytomegalovirus

Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that causes birth defects in newborns and life-threatening complications in immunocompromised individuals. Among all human herpesviruses, HCMV contains a much larger dsDNA genome within a similarly-sized capsid compared to the others, and it was proposed to require pp150, a tegument protein only found in cytomegaloviruses, to stabilize its genome-containing capsid. However, little is known about how pp150 interacts with the underlying capsid. Moreover, the smallest capsid protein (SCP), while dispensable in herpes simplex virus type 1, was shown to play essential, yet undefined, role in HCMV infection. Here, by cryo electron microscopy (cryoEM), we determine three-dimensional structures of HCMV capsid (no pp150) and virion (with pp150) at sub-nanometer resolution. Comparison of these two structures reveals that each pp150 tegument density is composed of two helix bundles connected by a long central helix. Correlation between the resolved helices and sequence-based secondary structure prediction maps the tegument density to the N-terminal half of pp150. The structures also show that SCP mediates interactions between the capsid and pp150 at the upper helix bundle of pp150. Consistent with this structural observation, ribozyme inhibition of SCP expression in HCMV-infected cells impairs the formation of DNA-containing viral particles and reduces viral yield by 10,000 fold. By cryoEM reconstruction of the resulting “SCP-deficient” viral particles, we further demonstrate that SCP is required for pp150 functionally binding to the capsid. Together, our structural and biochemical results point to a mechanism whereby SCP recruits pp150 to stabilize genome-containing capsid for the production of infectious HCMV virion.
GIS Development in China's Urban Governance: A Case Study of Shenzhen

Government agencies have been an important actor in using GIS and other information technologies across the world. However, contextual examinations of government GIS practices over time within non‐Western contexts remain sparse in the existing GIScience literature. In particular, little is known with respect to China's significant growth of using GIS in its urban government amidst its rapid urbanization and enormous transformation. This article presents an in‐depth investigation of the case of Shenzhen city, one of the China's leading cities in urban government GIS development. Drawing upon critical GIS research and GIS implementation studies, a synthesized theoretical framework is developed to interrogate the nature and evolutionary process of Shenzhen's government GIS practices. The analysis is focused on examining the role of broader social conditions, local contextual factors and organizational characteristics in shaping GIS development in Shenzhen's urban governance. Situated in this contextual analysis, this article also illustrates the three major transformations of GIS development in Shenzhen's planning agency over the past decade. The findings show that GIS development in Chinese urban governance has been influenced not only by the instrumental functions of GIS, but also by the interactions and relationships among different actors and institutions with various vested interests in the process of structuring and governing the urban spaces. This study will contribute to the ongoing discussion of understanding the interwoven relationship between GIS and society in GIScience research.
A functional NF-kappaB binding site in the human papillomavirus type 16 long control region.

By computer search, we identified one potential NF-kappaB binding site in the HPV16 long control region (LCR) at position 7554-7563 having two mismatches in comparison to the consensus NF-kappaB binding site of the Igkappa L promoter. Bandshift experiments with nuclear extracts from HeLa cells or purified glutathione S-transferase-p65 fusion protein clearly demonstrated that NF-kappaB is able to bind to this region of the LCR. However, in comparison to NF-kappaB binding on a consensus probe, the affinity of NF-kappaB for this site is about 250-fold reduced. When mutations were introduced into this NF-kappaB binding site, the activity of the LCR was increased, strongly suggesting that NF-kappaB was acting as a transcriptional repressor in the context of the HPV16 LCR. In addition, overexpression of NF-kappaB p65 repressed the activity of the HPV16 LCR, strengthening this conclusion.
GIS-Based Evaluation of Spatial Interactions by Geographic Disproportionality of Industrial Diversity

Diversity of regional industry is regarded as a key factor for regional development, as it has a positive relationship with economic stability, which attracts population. This paper focuses on how the spatial imbalance of industrial diversity contributes to the population change caused by inter-regional migration. This paper introduces a spatial interaction model for the Geographic Information System (GIS)-based simulation of the spatial interactions to evaluate the demographic attraction force. The proposed model adopts the notions of gravity, entropy, and virtual work. An industrial classification by profit level is introduced and its diversity is quantified with the entropy of information theory. The introduced model is applied to the cases of 207 regions in South Korea. Spatial interactions are simulated with an optimized model and their resultant forces, the demographic attraction forces, are compared with observed net migration for verification. The results show that the evaluated attraction forces from industrial diversity have a very significant, positive, and moderate relationship with net migration, while other conventional factors of industry, population, economy, and the job market do not. This paper concludes that the geographical quality of industrial diversity has positive and significant effects on population change by migration.
Genome-wide profiling at methylated promoters in pancreatic adenocarcinoma

Many genes undergo aberrant methylation in human cancers, and microarray platforms enable more comprehensive profiling of aberrant DNA methylation patterns. Methods: We used methylated CpG island amplification (MCA) and Agilent promoter and CpG island microarrays to identify differential DNA methylation patterns in pancreatic cancer vs. normal pancreas. We examined MCA array reproducibility, compared it to methylation profiles obtained using a cocktail of methylation-sensitive restriction enzymes and examined gene expression of methylated genes Results: 1,010 of 87,922 probes on the 88K promoter array (606 genes) had a higher signal (log2>2) in the pancreatic cancer line, Panc-1 compared to the non-neoplastic pancreatic duct line, HPDE. Using this cut-off, bisulfite sequencing and/or MSP confirmed differential methylation of all 27 genes (66 probes) predicted to be methylated by the MCA array. More than Â½ of the genes aberrantly hypermethylated in Panc-1 were not expressed in the pancreatic duct (HPDE) by expression array analysis. Using the 244K CpG island array, 1,968 CpG islands were differentially methylated in MiaPaca2 compared to normal pancreas. The MCA method was more likely to identify hypermethylation within CpG islands than a cocktail of methylation sensitive restriction enzymes. DNA methylation profiles using 10ng of DNA were highly correlated with those obtained 4 using 5ug of DNA (R2=0.98). Analysis of 57 pancreatic cancers and 34 normal pancreata using MSP identified MDFI, hsa-miR-9-1, ZNF415, CNTNAP2 and ELOVL4 as methylated in 96%, 89%, 86%, 82% and 68% of the cancers vs. 9%, 15%, 6%, 3% and 9% of normal pancreata, respectively. Conclusion: Promoter and CpG island array analysis finds aberrant methylation of hundreds of promoters and CpG islands in pancreatic cancer cells.
Impact of mud aggregate processes in sediment transport studies

PURPOSE: The goal of this Coastal and Hydraulics Engineering Technical Note (CHETN) is to communicate the effect of aggregated fine sediment on U.S. Army Corps of Engineers (USACE) mission areas, highlight research underway to quantify aggregate transport processes, and communicate the relevance and importance of these processes to project engineers within the USACE and other agencies.
Color-discrimination threshold determination using pseudoisochromatic test plates

We produced a set of pseudoisochromatic plates for determining individual color-difference thresholds to assess test performance and test properties, and analyzed the results. We report a high test validity and classification ability for the deficiency type and severity level [comparable to that of the fourth edition of the Hardy–Rand–Rittler (HRR) test]. We discuss changes of the acceptable chromatic shifts from the protan and deutan confusion lines along the CIE xy diagram, and the high correlation of individual color-difference thresholds and the red–green discrimination index. Color vision was tested using an Oculus HMC anomaloscope, a Farnsworth D15, and an HRR test on 273 schoolchildren, and 57 other subjects with previously diagnosed red–green color-vision deficiency.