Miracle-dz/UniFAR-FTUs huggingface dataset:
Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency

Persistence of a reservoir of latently infected memory T cells provides a barrier to HIV eradication in treated patients. Several reports have implicated the involvement of SWI/SNF chromatin remodeling complexes in restricting early steps in HIV infection, in coupling the processes of integration and remodeling, and in promoter/LTR transcription activation and repression. However, the mechanism behind the seemingly contradictory involvement of SWI/SNF in the HIV life cycle remains unclear. Here we addressed the role of SWI/SNF in regulation of the latent HIV LTR before and after transcriptional activation. We determined the predicted nucleosome affinity of the LTR sequence and found a striking reverse correlation when compared to the strictly positioned in vivo LTR nucleosomal structure; sequences encompassing the DNase hypersensitive regions displayed the highest nucleosome affinity, while the strictly positioned nucleosomes displayed lower affinity for nucleosome formation. To examine the mechanism behind this reverse correlation, we used a combinatorial approach to determine DNA accessibility, histone occupancy, and the unique recruitment and requirement of BAF and PBAF, two functionally distinct subclasses of SWI/SNF at the LTR of HIV-infected cells before and after activation. We find that establishment and maintenance of HIV latency requires BAF, which removes a preferred nucleosome from DHS1 to position the repressive nucleosome-1 over energetically sub-optimal sequences. Depletion of BAF resulted in de-repression of HIV latency concomitant with a dramatic alteration in the LTR nucleosome profile as determined by high resolution MNase nucleosomal mapping. Upon activation, BAF was lost from the HIV promoter, while PBAF was selectively recruited by acetylated Tat to facilitate LTR transcription. Thus BAF and PBAF, recruited during different stages of the HIV life cycle, display opposing function on the HIV promoter. Our data point to the ATP-dependent BRG1 component of BAF as a putative therapeutic target to deplete the latent reservoir in patients.
Protein Z plasma levels are not associated with the risk of coronary heart disease: the PRIME Study

** To cite this article: Morange PE, Juhan-Vague I on behalf of the PRIME Study Group. Protein Z plasma levels are not associated with the risk of coronary heart disease: the PRIME Study. J Thromb Haemost 2004; 2: 2050–1.
Laparoscopic versus open orchidopexy in children with intra-abdominal testes.

BACKGROUND/PURPOSE The management of intra-abdominal testis has been controversial but has changed significantly since the introduction of the laparoscopic technique. The aim of our study was to evaluate the success rate of laparoscopic orchidopexy (LO) compared with that of open orchidopexy (OO). MATERIALS AND METHODS In Kuopio University Hospital, 35 of 357 children with undescended testes treated between January 1992 and December 2004 had intra-abdominal testes. A retrospective review was performed to compare the outcomes of children having LO with those who had undergone OO. RESULTS Sixteen children with 19 intra-abdominal testes underwent LO and 18 children with 18 intra-abdominal testes underwent OO. Primary LO was performed in 14 children with 17 testes and staged Fowler-Stephens LO in 2 children. One LO was converted to OO. The mean (+/- standard deviation) operating time was 62 (+/- 30) minutes in the LO group and 43 (+/- 12) minutes in the OO-group (mean difference of 19 minutes, 95% confidence interval of the difference of 2 to 34 minutes; P = 0.025). There were no differences in the length of hospital stay between the two groups. Two major intra-abdominal complications occurred: 1 child in the LO-group had spermatic vessels torn, which led to a one-stage Fowler-Stephens orchidopexy, and the other child, one who had undergone a conversion from LO to OO, had a transection of the vas. One child in both groups was lost to follow-up. The overall success rate (acceptable scrotal position of the testis without testicular atrophy) was 88% in the LO group and 82% in the OO group. CONCLUSIONS Although marginally longer in duration, primary LO appears to be a feasible, safe technique for the management of the low intra-abdominal testes, whereas the staged Fowler-Stephens LO may be more safe than primary LO in cases with high intra-abdominal testes.
Intracellular identification of central noradrenergic and serotonergic neurons by a new double labeling procedure

The purpose of this study was to ascertain the identity of presumed noradrenergic or serotonergic neurons recorded by single cell techniques in the mammalian brain. A double labeling method was developed in which intracellular injections of a red fluorescing dye (ethidium bromide) could be co-localized with the formaldehyde-induced green fluorescence of norepinephrine or yellow fluorescence of serotonin. By this method, neurons of the rat locus coeruleus that display a characteristic activation-inhibition response to noxious stimuli were confirmed to be noradrenergic; the slow, rhythmically firing neurons of the dorsal raphe nucleus were confirmed to be serotonergic.
Is allorecognition specificity in Hydractinia symbiolongicarpus controlled by a single gene?

I N many benthic, colonial invertebrates, the capacity to distinguish conspecific self from nonself, or allorecognition, plays a crucial role in determining the nature and outcome of somatic, and perhaps gametic, interactions (BUSS 1982, 1990; GROSBERG 1988). One of the most striking features of invertebrate allorecognition systems is the extraordinary precision with which self can be distinguished from nonself, even in very large populations. To the extent that allorecognition specificity is heritable, this precision suggests that populations of colonial invertebrates carry unusually high levels of genetic variation, rivalling levels found at MHC Class I and I1 loci (e.g., Pons and WAKELAND 1990; PARHAM and OHTA 1996) and self-incompatibility loci in angiosperms (reviewed in CHARLESWORTH 1995). However, unlike the vertebrate major histocompatibility complex, or many plant self-incompatibility systems, the question of whether one or a few loci (with high levels of allelic diversity) or multiple loci (with more modest amounts of variation per locus) control invertebrate allorecognition remains largely unexplored. Some of the first attempts to decipher the formal genetics of invertebrate allorecognition met with considerable success. For example, among ascidians in the genera Botryllus and Botrylloides, a single locus with multiple codominant alleles appears to control the acute fusion/ rejection response; juxtaposed individuals sharing one or both alleles at this locus somatically fuse, whereas those not sharing an allele reject each other (OKA and WATA-
NCAA Division I Athletic Trainers' Perceptions and Use of Psychological Skills during Injury Rehabilitation

Applied sport psychology research suggests that the use of psychological skills (e.g., positive self-talk, goal-setting, relaxation) during the rehabilitation process increase recovery rates, increase adherence to rehabilitation, and decrease anxiety and stress (Heaney, 2006). Certified athletic trainers (ATCs) hold a critical role within injury rehabilitation as the primary health care professional who interacts with injured athletes. Therefore, properly trained, ATCs have been identified as the ideal professional to implement psychological skills during injury rehabilitation (Larson, Starkey, & Zaichkowsky, 1996). The purpose of this study was to explore National Collegiate Athletic Association (NCAA) Division I (D-I) ATCs use of psychological skills and perceptions of qualifications to implement psychological skills with athletes during rehabilitation. Results revealed that participants reported using goal-setting, communication, and time management most frequently with athletes. Results of a stepwise multiple regression analysis revealed that participants confidence in their ability to effectively demonstrate psychological skills significantly predicted their use of psychological skills, along with perceptions of the effectiveness of psychological skills and previous level of training in sport psychology. Lastly, participants perceived psychologists to be the most qualified professional to implement psychological skills with injured athletes. Implications for ATCs and sport psychology professionals are education. This includes ATCs educational requirements to be more detailed and clear for athletic training students as well as education by sport psychology consultants to help other professional better understand their role in the overall sport team.
Aligning context-based statistical models of language with brain activity during reading

Many statistical models for natural language processing exist, including context-based neural networks that (1) model the previously seen context as a latent feature vector, (2) integrate successive words into the context using some learned representation (embedding), and (3) compute output probabilities for incoming words given the context. On the other hand, brain imaging studies have suggested that during reading, the brain (a) continuously builds a context from the successive words and every time it encounters a word it (b) fetches its properties from memory and (c) integrates it with the previous context with a degree of effort that is inversely proportional to how probable the word is. This hints to a parallelism between the neural networks and the brain in modeling context (1 and a), representing the incoming words (2 and b) and integrating it (3 and c). We explore this parallelism to better understand the brain processes and the neural networks representations. We study the alignment between the latent vectors used by neural networks and brain activity observed via Magnetoencephalography (MEG) when subjects read a story. For that purpose we apply the neural network to the same text the subjects are reading, and explore the ability of these three vector representations to predict the observed word-by-word brain activity. Our novel results show that: before a new word i is read, brain activity is well predicted by the neural network latent representation of context and the predictability decreases as the brain integrates the word and changes its own representation of context. Secondly, the neural network embedding of word i can predict the MEG activity when word i is presented to the subject, revealing that it is correlated with the brain’s own representation of word i. Moreover, we obtain that the activity is predicted in different regions of the brain with varying delay. The delay is consistent with the placement of each region on the processing pathway that starts in the visual cortex and moves to higher level regions. Finally, we show that the output probability computed by the neural networks agrees with the brain’s own assessment of the probability of word i, as it can be used to predict the brain activity after the word i’s properties have been fetched from memory and the brain is in the process of integrating it into the context.
Isolation and Preliminary Characterization of Temperature-Sensitive Mutants of Influenza Virus

Isolation of temperature-sensitive (ts) mutants was attempted from the WSN strain of influenza A virus which was grown and assayed in MDBK cells. After growth of wild-type virus in the presence of 5-fluorouracil, 15 ts mutants were selected for which the ratio of plaquing efficiency at 39.5 C to that at 33 C was 10−3 or less. In pairwise crosses of ts mutants, recombination and complementation were either very efficient or undetectable. It is suggested, therefore, that the viral genome consists of physically discrete units and recombination occurs as an exchange of these units. All 15 mutants have been assigned with certainty into five recombination groups. Three mutants are suspected to be double mutants. Any two complementing mutants always recombined with each other, and noncomplementing mutants did not recombine. In physiological tests, mutants showed diverse patterns of functional defects at the nonpermissive temperature. However, it was not always possible to correlate these physiological defects with the results of genetic characterization.
Impact of Adjuvant Chemotherapy in Elderly Breast Patients in Taiwan, A Hospital-Based Study

Purpose: Decisions as to whether to provide adjuvant treatment in older breast cancer patients remains challenging. Side effects of chemotherapy have to be weighed against life expectancy, comorbidities, functional status, and frailty. To aid decision-making, we retrospectively analyzed 110 women with breast cancer treated with a curative intention from 2006 to 2012. Survival data with clinical and pathological parameters were evaluated to address the role of adjuvant chemotherapy in this study population. Method: A total of 110 elderly (>70 years) patients that received mastectomy at two hospitals in Taiwan were observed retrospectively for a medium of 51 months. After mastectomy, patients received conservative treatment or adjuvant chemotherapy, or hormone therapy following clinical guidelines or physician’s preference. Data were collected from the cancer registry system. Results: Median age at diagnosis was 75.7 years. Thirty-five percent of patients received adjuvant chemotherapy, these having a significantly younger age (mean=74.0±5.3 vs 77.5±5.3, p<0.001) and higher tumor staging (p=0.003) compared with their non-chemotherapy counterparts. Five-year overall survival was non-significantly higher in patients who received adjuvant chemotherapy (with chemotherapy 64.2% vs without chemotherapy 62.6%, p=0.635), while five-year recurrence free survival was non-significantly lower (with chemotherapy 64.1% vs without chemotherapy 90.5%, p=0.80). Conclusions: In this analysis, adjuvant chemotherapy tended to be given to patients with a younger age and higher tumor staging at our institute. It was not associated with any statistically significant improvement in survival and recurrence rate. Until age specific recommendations are available, physicians must use their clinical judgment and assess the tumor biology with the patient’s comorbidities to make the best choice. Clinical trials focusing on this critical issue are warranted.
Memory Matters: Contexts for Understanding Sexual Abuse Recollections, Edited by Janice Haaken and Paula Reavey (2010) Psychology Press Chapter four: Speaking up against justice: credibility, suggestibility and children’s memory on trial

Introduction Judge: And if you do always tell the truth where will you go when you die? Girl: Up to heaven sir. Judge: And what will become of you if you tell lies? Girl: I shall go down to the naughty place, sir. Judge: Are you quite sure of that? Girl: Yes, sir. Judge: Let her be sworn, it is quite clear that she knows more than I do! (Mr Justice Maule (1788-1858) examining a young witness on the nature of the oath, quote as Spencer & Flin 1993, p.51).
Characterization of cytoskeleton-enriched protein fraction of the trabecular meshwork and ciliary muscle cells.

PURPOSE To understand the molecular basis for the known distinct contractile characteristics of trabecular meshwork (TM) and ciliary muscle (CM) cells, the cytoskeleton-enriched protein fractions of the TM and CM cells were isolated and characterized. METHODS The nonionic surfactant insoluble fraction enriched for cytoskeletal proteins was isolated from human and porcine TM tissue and cells and from CM cells and was characterized by SDS-PAGE, mass spectrometry, and immunoblotting techniques. RESULTS The cytoskeleton-enriched protein fraction derived from both human and porcine TM cells contained Plectin 1, Filamin A, non-muscle myosin IIA, clathrin, α-actinin, vimentin, actin, caldesmon, myosin IC, and annexin A2 as major proteins and was noted to exhibit compositional similarity with the cytoskeletal protein fraction isolated from TM tissue. Importantly, the cytoskeletal protein composition of the TM cells was also found to be similar to that noted for CM and vascular endothelial cells. Although the activity of myosin II, a crucial regulator of cellular contraction and a major component of the cytoskeletal protein fraction in TM and CM cells, was regulated predominantly by Rho kinase in both cell types, myosin light chain kinase (MLCK) also appeared to control myosin II activity in CM cells. CONCLUSIONS These data reveal that the activity of non-muscle myosin II, a critical molecule of cellular contraction, was found to be regulated differentially in TM and CM cells by the Rho kinase and the MLCK pathways despite their compositional similarity in cytoskeletal protein profile.
Rheological Differences of Waxy Barley Flour Dispersions Mixed with Various Gums

Rheological properties of waxy barley flour (WBF) dispersions mixed with various gums (carboxyl methyl celluleose, guar gum, gum arabic, konjac gum, locust bean gum, tara gum, and xanthan gum) at different gum concentrations were examined in steady and dynamic shear. WBF-gum mixture samples showed a clear trend of shear-thinning behavior and had a non-Newtonian nature with yield stress. Rheological tests indicated that the flow and dynamic rheological parameter (apparent viscosity, consistency index, yield stress, storage modulus, and loss modulus) values of WBF dispersions mixed with gums, except for gum arabic, were significantly higher than those of WBF with no gum, and also increased with an increase in gum concentration. In particular, konjac gum at 0.6% among other gums showed the highest rheological parameter values. Tan δ values of WBF-xanthan gum mixtures were lower than those of other gums, showing that there is a more pronounced synergistic effect on the elastic properties of WBF in the presence of xanthan gum. Such synergistic effect was hypothesized by considering thermodynamic compatibility between xanthan gum and WBF. These rheological results suggest that in the WBF-gum mixture systems, the addition of gums modified the flow and viscoelastic properties of WBF, and that these modifications were dependent on the type of gum and gum concentration.
Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages

Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food. miRNAs are tiny riboregulator of gene expression by either decreasing and/or increasing the expression of their corresponding target genes. Despite several works on identification and functional characterization of plant miRNAs, the role of miRNAs in the regulation of isoflavones metabolism is still a virgin field. In the present study, we identified a total of 31 new miRNAs along with their 245 putative target genes from soybean seed-specific ESTs using computational approach. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates metabolism and genetic information processing. Out of that, a total of 5 miRNAs (Gma-miRNA12, Gma-miRNA24, Gma-miRNA26, Gma-miRNA28, and Gma-miRNA29) were predicted and validated for their probable role during isoflavone biosynthesis. We also validated their five target genes using RA-PCR, which is as good as 5'RLM-RACE. Temporal regulation [35 days after flowering, 45, 55, and 65 DAF] of miRNAs and their targets showed differential expression schema. Differential expression of Gma-miR26 and Gma-miRNA28 along with their corresponding target genes (Glyma.10G197900 and Glyma.09G127200) showed a direct relationship with the total isoflavone content. Therefore, understanding the miRNA-based genetic regulation of isoflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isoflavone yield.
The Conventional Status of Reflexive Awareness: What's at Stake in a Tibetan Debate?

rJe Tsong khapa argues that consciousness is not intrinsically reflexive even conventionally, and reads Candrakīrti and Śāntideva as endorsing this view. 'Ju Mipham Rinpoche (1846-1912) criticizes Tsong khapa's argument and his reading of Candrakīrti, arguing that while ultimately consciousness is not intrinsically reflexive, conventionally it is. This article defends Tsong khapa's philosophy of mind and his hermeneutical strategy and shows that this debate is important both philosophically and doxographically.
C4 photosynthesis and water stress.

BACKGROUND In contrast to C(3) photosynthesis, the response of C(4) photosynthesis to water stress has been less-well studied in spite of the significant contribution of C(4) plants to the global carbon budget and food security. The key feature of C(4) photosynthesis is the operation of a CO(2)-concentrating mechanism in the leaves, which serves to saturate photosynthesis and suppress photorespiration in normal air. This article reviews the current state of understanding about the response of C(4) photosynthesis to water stress, including the interaction with elevated CO(2) concentration. Major gaps in our knowledge in this area are identified and further required research is suggested. SCOPE Evidence indicates that C(4) photosynthesis is highly sensitive to water stress. With declining leaf water status, CO(2) assimilation rate and stomatal conductance decrease rapidly and photosynthesis goes through three successive phases. The initial, mainly stomatal phase, may or may not be detected as a decline in assimilation rates depending on environmental conditions. This is because the CO(2)-concentrating mechanism is capable of saturating C(4) photosynthesis under relatively low intercellular CO(2) concentrations. In addition, photorespired CO(2) is likely to be refixed before escaping the bundle sheath. This is followed by a mixed stomatal and non-stomatal phase and, finally, a mainly non-stomatal phase. The main non-stomatal factors include reduced activity of photosynthetic enzymes; inhibition of nitrate assimilation, induction of early senescence, and changes to the leaf anatomy and ultrastructure. Results from the literature about CO(2) enrichment indicate that when C(4) plants experience drought in their natural environment, elevated CO(2) concentration alleviates the effect of water stress on plant productivity indirectly via improved soil moisture and plant water status as a result of decreased stomatal conductance and reduced leaf transpiration. CONCLUSIONS It is suggested that there is a limited capacity for photorespiration or the Mehler reaction to act as significant alternative electron sinks under water stress in C(4) photosynthesis. This may explain why C(4) photosynthesis is equally or even more sensitive to water stress than its C(3) counterpart in spite of the greater capacity and water use efficiency of the C(4) photosynthetic pathway.