Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vivo Analysis of Developmentally and Evolutionarily Dynamic Protein-DNA Interactions Regulating Transcription of the Pgk2 Gene during Mammalian Spermatogenesis

ABSTRACT Transcription of the testis-specific Pgk2 gene is selectively activated in primary spermatocytes to provide a source of phosphoglycerate kinase that is critical to normal motility and fertility of mammalian spermatozoa. We examined dynamic changes in protein-DNA interactions at the Pgk2 gene promoter during murine spermatogenesis in vivo by performing genomic footprinting and chromatin immunoprecipitation assays with enriched populations of murine spermatogenic cells at stages prior to, during, and following transcription of this gene. We found that genes encoding the testis-specific homeodomain factor PBX4 and its coactivator, PREP1, are expressed in patterns that mirror expression of the Pgk2 gene and that these factors become bound to the Pgk2 enhancer in cells in which this gene is actively expressed. We therefore suggest that these factors, along with CREM and SP3, direct stage- and cell type-specific transcription of the Pgk2 gene during spermatogenesis. We propose that binding of PBX4, plus its coactivator PREP1, is a rate-limiting step leading to the initiation of tissue-specific transcription of the Pgk2 gene. This study provides insight into the developmentally dynamic establishment of tissue-specific protein-DNA interactions in vivo. It also allows us to speculate about the events that led to tissue-specific regulation of the Pgk2 gene during mammalian evolution.
Prevalences of Shiga Toxin Subtypes and Selected Other Virulence Factors among Shiga-Toxigenic Escherichia coli Strains Isolated from Fresh Produce

ABSTRACT Shiga-toxigenic Escherichia coli (STEC) strains were isolated from a variety of fresh produce, but mostly from spinach, with an estimated prevalence rate of 0.5%. A panel of 132 produce STEC strains were characterized for the presence of virulence and putative virulence factor genes and for Shiga toxin subtypes. About 9% of the isolates were found to have the eae gene, which encodes the intimin binding protein, and most of these belonged to known pathogenic STEC serotypes, such as O157:H7 and O26:H11, or to serotypes that reportedly have caused human illness. Among the eae-negative strains, there were three O113:H21 strains and one O91:H21 strain, which historically have been implicated in illness and therefore may be of concern as well. The ehxA gene, which encodes enterohemolysin, was found in ∼60% of the isolates, and the saa and subAB genes, which encode STEC agglutinating adhesin and subtilase cytotoxin, respectively, were found in ∼30% of the isolates. However, the precise roles of these three putative virulence factors in STEC pathogenesis have not yet been fully established. The stx 1a and stx 2a subtypes were present in 22% and 56%, respectively, of the strains overall and were the most common subtypes among produce STEC strains. The stx 2d subtype was the second most common subtype (28% overall), followed by stx 2c (7.5%), and only 2 to 3% of the produce STEC strains had the stx 2e and stx 2g subtypes. Almost half of the produce STEC strains had only partial serotypes or were untyped, and most of those that were identified belonged to unremarkable serotypes. Considering the uncertainties of some of these Stx subtypes and putative virulence factors in causing human illness, it is difficult to determine the health risk of many of these produce STEC strains.
Point and Click, Carefully

This study investigated inconsistent responding to survey items by participants involved in longitudinal, web-based substance use research. We also examined cross-sectional and prospective predictors of inconsistent responding. Middle school (N = 1,023) and college students (N = 995) from multiple sites in the United States responded to online surveys assessing substance use and related variables in three waves of data collection. We applied a procedure for creating an index of inconsistent responding at each wave that involved identifying pairs of items with considerable redundancy and calculating discrepancies in responses to these items. Inconsistent responding was generally low in the Middle School sample and moderate in the College sample, with individuals showing only modest stability in inconsistent responding over time. Multiple regression analyses identified several baseline variables—including demographic, personality, and behavioral variables—that were uniquely associated with inconsistent responding both cross-sectionally and prospectively. Alcohol and substance involvement showed some bivariate associations with inconsistent responding, but these associations largely were accounted for by other factors. The results suggest that high levels of carelessness or inconsistency do not appear to characterize participants’ responses to longitudinal web-based surveys of substance use and support the use of inconsistency indices as a tool for identifying potentially problematic responders.
Dietary assessment of a population of pregnant women in Sheffield, UK

The present study examined the dietary intakes of a population of pregnant women living in the North of England. The objectives of the paper were to assess and describe the dietary intakes of the population and relate the findings to existing data on the diet of pregnant and non-pregnant women in the UK. A total of 250 pregnant women attending their first antenatal appointment at the Jessop Wing Hospital, Sheffield, UK were recruited. Information on their diet was assessed by an interviewer-administered semi-quantified food frequency questionnaire (FFQ). The mean intakes as assessed by the FFQ were similar to other studies of UK pregnant population; however Sheffield pregnant women had lower intakes of calcium and folate. Study findings were also related to the National Diet and Nutrition Survey and to the Estimated Nutrient Intakes (EAR). Of the study participants, 40 % did not meet the EAR for calcium, 67 % for iron and 69 % for folate. Subgroup comparisons suggested lower nutrient intakes of participants living in the 40 % most deprived electoral wards. The study findings suggest that the diet of pregnant women in Sheffield is characterised by low intakes of important nutrients for pregnancy such as folate and nutrient variations by electoral wards.
Dietary carbohydrates with different rates of fermentation affect fermentation end-product profiles in different sites of gastro-intestinal tract of weaning piglet

An in vivo experiment was conducted to examine changes in fermentation end-products in the gastro-intestinal tract (GIT) of weaning piglets by the inclusion of fermentable carbohydrates in the diet. The experiment was repeated in three replicates of 36 piglets. Piglets were raised free of antibiotics and creep feeding prior to weaning at 4 weeks of age. Each replicate was conducted over a period of 10 days. The piglets were offered one of two dietary treatments: control diet (CON), and fermentable carbohydrate enriched diet (CHO); and were subjected to one of the two fasting treatments (i) fasting for 2 days in the beginning of the experimental period and (ii) non-fasting. Piglets were slaughtered on the 1st, 4th and 10th day of each period. Digesta samples were collected from: first half of small intestine, second half of small intestine, caecum, and colon. The dry matter, volatile fatty acid (VFA) profile, and ammonia concentrations were analysed. Food intake, growth and food conversion ratio were also recorded. There were no differences in production performances such as growth and food conversion ratio (FCR) between the treatment groups. Concentrations of VFA were significantly higher, while ammonia concentration was significantly lower in the CHO group compared to the CON group in different fermentation sites within the GIT (P<0·001), and on different slaughtering days (P<0·05). Fasting had no effect on fermentation end-products. This study concludes that the addition of fermentable carbohydrates of varying fermentabilities stimulated carbohydrate fermentation, with reduction in protein fermentation along the different parts of GIT studied, in weaning piglets
Mitogen-Activated Protein Kinase Feedback Phosphorylation Regulates MEK1 Complex Formation and Activation during Cellular Adhesion

ABSTRACT Cell adhesion and spreading depend on activation of mitogen-activated kinase, which in turn is regulated both by growth factor and integrin signaling. Growth factors, such as epidermal growth factor, are capable of activating Ras and Raf, but integrin signaling is required to couple Raf to MEK and MEK to extracellular signal-regulated protein kinase (ERK). It was previously shown that Rac-p21-activated kinase (PAK) signaling regulated the physical association of MEK1 with ERK2 through phosphorylation sites in the proline-rich sequence (PRS) of MEK1. It was also shown that activation of MEK1 and ERK by integrins depends on PAK phosphorylation of S298 in the PRS. Here we report a novel MEK1-specific regulatory feedback mechanism that provides a means by which activated ERK can terminate continued PAK phosphorylation of MEK1. Activated ERK can phosphorylate T292 in the PRS, and this blocks the ability of PAK to phosphorylate S298 and of Rac-PAK signaling to enhance MEK1-ERK complex formation. Preventing ERK feedback phosphorylation on T292 during cellular adhesion prolonged phosphorylation of S298 by PAK and phosphorylation of S218 and S222, the MEK1 activating sites. We propose that activation of ERK during adhesion creates a feedback system in which ERK phosphorylates MEK1 on T292, and this in turn blocks additional S298 phosphorylation in response to integrin signaling.
The calorimetric criterion for a two‐state process revisited

The “calorimetric criterion” is one of the important experimental approaches for determining whether protein folding is an “all‐or‐none” two‐state transition (i.e., whether intermediates are present at equilibrium). The calorimetric criterion states that the equivalence of the “measured” calorimetric enthalpy change and the effective two‐state van't Hoff enthalpy change demonstrates that there is a two‐state transition. This paper addresses the essential question of whether the calorimetric criterion is a necessary and sufficient condition for a two‐state process and shows that it is necessary but not sufficient by means of specific examples. Analysis of simple models indicates that the heat capacity curve, regardless of whether it originates from a two‐state process or not, can always be decomposed in such a way that the calorimetric criterion is satisfied. Exact results for a three‐state model and a homopolymer tetramer demonstrate that the deviation from the calorimetric criterion is not simply related to the population of intermediate states. Analysis of a three‐helix bundle protein model, which has a two‐state folding from a random coil to ordered (molten) globule, shows that the calorimetric criterion may not be satisfied if the standard linear interpolation of baselines (weighted or unweighted) is employed. A specific example also suggests that the more recently introduced deconvolution method is not necessarily better than the simple calorimetric criterion for distinguishing a two‐state transition from a three‐state transition. Although the calorimetric criterion is not a sufficient condition for a two‐state process, it is likely to continue to be of practical utility, particularly when its results are shown to be consistent with those from other experimental methods.
Toward understanding the heterogeneity in obsessive-compulsive disorder: Evidence from narratives in adult patients

Background: Current attempts at understanding the heterogeneity in obsessive-compulsive disorder have relied on quantitative methods. The results of such work point toward a dimensional structure for obsessive-compulsive disorder. Existing qualitative work in obsessive-compulsive disorder has focused on understanding specific aspects of the obsessive-compulsive disorder experience in greater depth. However, qualitative methods are also of potential value in furthering our understanding of obsessive-compulsive disorder heterogeneity by allowing for open-ended exploration of the obsessive-compulsive disorder experience and correlating identified subtypes with patient narratives. Objective: We explored variations in patients’ experience prior to, during and immediately after performing their compulsions. Method: Semi-structured interviews were conducted with 20 adults with obsessive-compulsive disorder, followed by inductive thematic analysis. Participant responses were not analyzed within the context of an existing theoretical framework, and themes were labeled descriptively. Results: The previous dichotomy of ‘anxiety’ vs ‘incompleteness’ emerged organically during narrative analysis. In addition, we found that some individuals with obsessive-compulsive disorder utilized their behaviors as a way to cope with stress and anxiety more generally. Other participants did not share this experience and denied finding any comfort in their obsessive-compulsive behaviors. The consequences of attentional difficulties were highlighted, with some participants describing how difficulty focusing on a task could influence the need for it to be repeated multiple times. Conclusions: The extent to which patients use obsessive-compulsive disorder as a coping mechanism is a relevant distinction with potential implications for treatment engagement. Patients may experience ambivalence about suppressing behaviors that they have come to rely upon for management of stress and anxiety, even if these behaviors represent symptoms of a psychiatric illness.
Age at Deafening Affects the Stability of Learned Song in Adult Male Zebra Finches

Male zebra finches (Taeniopygia guttata) master the imitation of a song model 80–90 d after hatching and retain it with little change for the rest of their lives. Acquisition and maintenance of this imitation require intact hearing. A previous report showed that male zebra finches deafened as adults start to lose some of the acoustic and temporal features of their song a few weeks after deafening and that by 16 weeks the learned song is severely degraded (Nordeen and Nordeen, 1992). However, this previous study noted no correlation between the age at deafening and the subsequent timing and extent of song loss. We deafened adult male zebra finches ranging in age from 81 d to 6 years. The song of birds deafened at the younger ages (81–175 d) deteriorated severely after a few weeks, and within that age bracket, the older the bird was at deafening, the longer it took for this degradation to occur and the slower the subsequent process of song deterioration. The song of birds deafened at 2 years and older showed little change during the first 51 weeks after deafening but was grossly altered by 100 weeks. We suggest (1) that this age effect could be independent of experience or (2) that each time a bird sings, a little bit of learning—motor engrainment—occurs, adding to memory duration in a cumulative manner.
Thesis for the Degree of Doctor of Philosophy Formal and Informal Software Specifications

The topic of this thesis is to bridge the gap between formal and informal software specifications. Formal specifications are required for the use of formal methods to verify the correctness of software. If we expect formal methods to be used in realistic software development projects, we need to enable people with varying levels of familiarity with formal specification languages to understand, maintain and create formal specifications. To address these problems, we provide a tool for translating specifications written in the formal language OCL, a substandard of UML, to natural language. We also provide a multilingual, syntax-directed editor where OCL and natural language specifications can be edited in parallel. The implementation of our work is to a large extent based on the Grammatical Framework (GF). GF is a grammar formalism based on type theory, which provides a special purpose language for defining grammars, and a compiler for this language. We have developed a GF grammar for specifications in OCL and natural language. The grammar captures the OCL type system, its built-in constructions and the predefined types of the OCL library. It is dynamically extended with domain-specific concepts by generating GF grammar modules from UML class diagrams. The generated modules make use of a grammar-level API of common constructions, which means that these modules can be modified without requiring GF expertise. To improve the readability of the translation of OCL specifications, the grammar includes formatting of the produced natural language. Inspired by Natural Language Generation techniques like aggregation, we also apply transformations to abstract syntax trees using a program external to the GF grammar. Our tool is a part of the KeY system, which integrates formal software specification and verification into the industrial software engineering processes. The tool has successfully been used for a non-trivial case study: translating the OCL specifications of the Java Card API into English.
Effect of mercury and organomercurials on cellular glucose utilization: a study using resting mercury‐resistant yeast cells

Aims: Mercury compounds are highly toxic to all types of living cells. Isolated yeast strains of Rhodotorula rubra showed high and low resistance pattern towards mercury and organomercurial compounds. To investigate the basis of differential sensitivity of these two types of strains, glucose utilization was measured in the presence of mercury compounds.
Effect of instantaneous frequency glides on interaural time difference processing by auditory coincidence detectors

Detecting interaural time difference (ITD) is crucial for sound localization. The temporal accuracy required to detect ITD, and how ITD is initially encoded, continue to puzzle scientists. A fundamental question is whether the monaural inputs to the binaural ITD detectors differ only in their timing, when temporal and spectral tunings are largely inseparable in the auditory pathway. Here, we investigate the spectrotemporal selectivity of the monaural inputs to ITD detector neurons of the owl. We found that these inputs are selective for instantaneous frequency glides. Modeling shows that ITD tuning depends strongly on whether the monaural inputs are spectrotemporally matched, an effect that may generalize to mammals. We compare the spectrotemporal selectivity of monaural inputs of ITD detector neurons in vivo, demonstrating that their selectivity matches. Finally, we show that this refinement can develop through spike timing-dependent plasticity. Our findings raise the unexplored issue of time-dependent frequency tuning in auditory coincidence detectors and offer a unifying perspective.
Decreased Expression of Breast Cancer Resistance Protein in the Duodenum in Patients with Obstructive Cholestasis

Background/Aims: The expression of transporters involved in bile acid homeostasis is differentially regulated during obstructive cholestasis. Since the drug efflux transporter breast cancer resistance protein (BCRP) is known to transport bile acids, we investigated whether duodenal BCRP expression could be altered during cholestasis. Methods: Using real-time RT-PCR analysis we determined mRNA expression levels in duodenal tissue of 19 cholestatic patients. Expression levels were compared to 14 healthy subjects. BCRP protein staining was determined in biopsies of 6 cholestatic and 6 healthy subjects by immunohistochemistry. Results: We found that in patients with obstructive cholestasis mean duodenal BCRP mRNA levels were significantly reduced to 53% and mean protein staining was reduced to 57%. Conclusions: BCRP, a transporter for bile acids and numerous drugs, appears to be down-regulated in the human duodenum during cholestasis. The clinical impact of these results has to be investigated in further studies.
Behavioral and electrophysiological effects of endocannabinoid and dopaminergic systems on salient stimuli

Rewarding effects have been related to enhanced dopamine (DA) release in corticolimbic and basal ganglia structures. The DAergic and endocannabinoid interaction in the responses to reward is described. This study investigated the link between endocannabinoid and DAergic transmission in the processes that are related to response to two types of reward, palatable food and novelty. Mice treated with drugs acting on endocannabinoid system (ECS) (URB597, AM251) or DAergic system (haloperidol) were submitted to approach-avoidance conflict tasks with palatable food or novelty. In the same mice, the cannabinoid type-1 (CB1)-mediated GABAergic transmission in medium spiny neurons of the dorsomedial striatum was analyzed. The endocannabinoid potentiation by URB597 magnified approach behavior for reward (food and novelty) and in parallel inhibited dorsostriatal GABAergic neurotransmission. The decreased activity of CB1 receptor by AM251 (alone or with URB597) or of DAergic D2 receptor by haloperidol had inhibitory effects toward the reward and did not permit the inhibition of dorsostriatal GABAergic transmission. When haloperidol was coadministered with URB597, a restoration effect on reward and reward-dependent motor activity was observed, only if the reward was the palatable food. In parallel, the coadministration led to restoring inhibition of CB1-mediated GABAergic transmission. Thus, in the presence of simultaneous ECS activation and inhibition of DAergic system the response to reward appears to be a stimulus-dependent manner.
Implications of device diversity for organic localization

Many indoor localization methods are based on the association of 802.11 wireless RF signals from wireless access points (WAPs) with location labels. An “organic” RF positioning system relies on regular users, not dedicated surveyors, to build the map of RF fingerprints to location labels. However, signal variation due to device heterogeneity may degrade localization performance. We analyze the diversity of those signal characteristics pertinent to indoor localization — signal strength and AP detection — as measured by a variety of 802.11 devices. We first analyze signal strength diversity, and show that pairwise linear transformation alone does not solve the problem. We propose kernel estimation with a wide kernel width to reduce the difference in probability estimates. We also investigate diversity in access point detection. We demonstrate that localization performance may degrade significantly when AP detection rate is used as a feature for localization, and correlate the loss of performance to a device dissimilarity measure captured by Kullback-Leibler divergence. Based on this analysis, we show that using only signal strength, without incorporating negative evidence, achieves good localization performance when devices are heterogeneous.