Miracle-dz/UniFAR-FTUs huggingface dataset:
Two bHLH-type transcription factors, JA-ASSOCIATED MYC2-LIKE2 and JAM3, are transcriptional repressors and affect male fertility

The jasmonate (JA) plant hormones regulate responses to biotic and abiotic stress and aspects of plant development, including male fertility in Arabidopsis thaliana. The bHLH-type transcription factor JA-ASSOCIATED MYC2-LIKE1 (JAM1) negatively regulates JA signaling and gain-of-function JAM1 transgenic plants have impaired JA-mediated male fertility. Here we report that JAM2 and JAM3, 2 bHLHs closely related to JAM1, also act as transcriptional repressors. Moreover, overexpression of JAM2 and JAM3 also results in reduced male fertility. These results suggest that JAM1, JAM2, and JAM3 act redundantly as negative regulators of JA-mediated male fertility.
Clinical examination following preoperative chemoradiation for rectal cancer is not a reliable surrogate end point.

PURPOSE Clinical assessment of rectal cancer response to preoperative combined-modality therapy (CMT) using digital rectal examination (DRE) has been proposed as a means of assessing efficacy of therapy. However, because the accuracy of this approach has not been established, we conducted a prospective analysis to determine the operating surgeon's ability to assess response using DRE. PATIENTS AND METHODS Ninety-four prospectively accrued patients with locally advanced rectal cancer (T3/4 or N1) were evaluated with DRE and sigmoidoscopy in order to determine the following tumor characteristics: size, location, mobility, morphology, and circumference. Following preoperative CMT (50.40 Gy with fluorouracil-based chemotherapy) and under general anesthesia, the same surgeon estimated tumor response based on changes in these tumor characteristics, assessed via DRE. Percent pathologic tumor response was determined prospectively by a single pathologist using whole mount sections of the resected cancer. RESULTS Clinical assessment using DRE underestimated pathologic response in 73 cases (78%). In addition, DRE was able to identify only 3 of 14 cases (21%) with a pathologic complete response. There were no clinical overestimates of response. None of the clinicopathologic tumor characteristics examined had a significant impact on DRE estimation of response. CONCLUSION Clinical examination underestimates the extent of rectal cancer response to preoperative CMT. Given the inaccuracy of DRE following preoperative CMT, it should not be used as a sole means of assessing efficacy of therapy nor for selecting patients following CMT for local surgical therapies.
A Prospective Assessment of Nasopharyngolaryngoscope Recording Adaptor Use in Residency Training

Flexible fiberoptic nasopharyngolaryngoscope (FN) examinations are important to the practice of otolaryngology (ENT). We sought to assess whether a portable recording adaptor for the FN can enhance resident learning and improve patient management. The adaptor was used prospectively on consultations by first- and second-year ENT residents, and changes in diagnosis and management were recorded in the patient care workflow. In 43 patients, we found a 23% change in diagnosis, 44% change in management, and 19% change in surgical management after an attending reviewed recorded videos. Residents and attendings reported that discussing the video enhanced learning in 88% and 81% of cases, respectively. A portable FN recording adaptor has the potential to improve resident training and perhaps lead to more prompt health care delivery.
Sirolimus in Kidney Transplantation Indications and Practical Guidelines: De novo Sirolimus-Based Therapy Without Calcineurin Inhibitors

A de novo calcineurin inhibitor avoidance regimen based on sirolimus has been successfully used worldwide; demonstrating improved renal function from 1 to 5 years. This includes use of an induction antibody followed by sirolimus, mycophenolate mofetil, and steroids. This combination has a somewhat different side effect profile and wider experience has revealed that the use of de novo sirolimus requires careful therapeutic drug level monitoring, especially the first 6 months posttransplant. Experience has also demonstrated that delaying the introduction of sirolimus in patients considered at high risk for early mammalian target of rapamycin associated complications will optimize these results. For such recipients, the initial use of a calcineurin inhibitor drug for 2 to 4 months is preferred, followed by conversion to sirolimus. The late withdrawal of steroids may be possible, but awaits further evaluation in randomized controlled trials.
An IL-13 Promoter Polymorphism Associated with Liver Fibrosis in Patients with Schistosoma japonicum

The aim of this study was to determine whether two polymorphisms in the gene encoding IL13 previously associated with Schistosoma hematobium (S. hematobium) and S. mansoni infection are associated with S. japonicum infection. Single nucleotide polymorphisms (SNPs) rs1800925 (IL13/-1112C>T) and rs20541 (IL13R130Q) were genotyped in 947 unrelated individuals (307 chronically infected, 339 late-stage with liver fibrosis, 301 uninfected controls) from a schistosomiasis-endemic area of Hubei province in China. Regression models were used to evaluate allelic and haplotypic associations with chronic and late-stage schistosomiasis adjusted for non-genetic covariates. Expression of IL-13 was measured in S. japonicun-infected liver fibrosis tissue and normal liver tissue from uninfected controls by immunohistochemistry (IHC). The role of rs1800925 in IL-13 transcription was further determined by Luciferase report assay using the recombinant PGL4.17-rs180092 plasmid. We found SNP rs1800925T was associated with late-stage schistosomiasis caused by S. japonicum but not chronic schistosomiasis (OR = 1.39, 95%CI = 1.02–1.91, p = 0.03) and uninfected controls (OR = 1.49, 95%CI = 1.03–2.13, p = 0.03). Moreover, the haplotype rs1800925T-rs20541C increased the risk of disease progression to late-stage schistosomiasis (OR = 1.46, p = 0.035), whereas haplotype rs1800925C-rs20541A showed a protective role against development of late-stage schistosomiasis (F = 0.188, OR = 0.61, p = 0.002). Furthermore, S. japonicum-induced fibrotic liver tissue had higher IL13 expression than normal liver tissue. Plasmid PGL4.17-rs1800925T showed a stronger relative luciferase activity than Plasmid PGL4.17-rs1800925C in 293FT, QSG-7701 and HL-7702 cell lines. In conclusion, the functional IL13 polymorphism, rs1800925T, previously associated with risk of schistosomiasis, also contributes to risk of late-stage schistosomiasis caused by S. japonicum.
Histopathological Grading Systems In Oral Squamous Cell Carcinoma : A Review

: The prognostic value of histopathologic grading of oral squamous cell carcinomas (SCC) has varied from not any to highly significant. BRODERS' method of grading was compared with a modification of a recent malignancy grading system recommended by ANNEROTH et al. which was performed only within the histologically most invasive areas of the tumors. Cox's multivariate survival analyses showed that this grading in the invasive sites had highly significant prognostic value. BRODERS grade had no prognostic value. The stage of tumor had also prognostic value. Bryne M. presented a hypothesis suggesting that molecular and morphological characteristics at the invasive front area of various squamous cell carcinomas may reflect tumor prognosis better than other parts of the tumor. He further states that several molecular events of importance for tumor spread. These highly significant results indicate that the histologically invasive areas may be primarily responsible for the clinical behavior of the tumor, and this may be of importance for the choice of therapy for oral SCC.
Profiles of vocal development in young cochlear implant recipients.

PURPOSE The main purpose of this investigation was to examine the effects of cochlear implant experience on prelinguistic vocal development in young deaf children. Procedure A prospective longitudinal research design was used to document the sequence and time course of vocal development in 7 children who were implanted between 10 and 36 months of age. Speech samples were collected twice before implant activation and on a monthly basis thereafter for up to 2 years. Children's vocalizations were classified according to the levels of the Stark Assessment of Early Vocal Development--Revised (SAEVD-R; S. Nathani, D. J Ertmer, & R. E. Stark, 2006). RESULTS The main findings were (a) 6 of 7 children made advancements in vocal development after implantation; (b) children implanted between 12 and 36 months progressed through SAEVD-R levels in the predicted sequence, whereas a child implanted at a younger age showed a different sequence; (c) milestones in vocal development were often achieved with fewer months of hearing experience than observed in typically developing infants and appeared to be influenced by age at implantation; and (d) in general, children implanted at younger ages completed vocal development at younger chronological ages than those implanted later in life. Specific indicators of benefit from implant use were also identified. CONCLUSION The time course of vocal development in young cochlear implant recipients can provide clinically useful information for assessing the benefits of implant experience. Studies of postimplantation vocal development have the potential to inform theories of spoken language development.
Anatomy of Herpes Simplex Virus DNA XII. Accumulation of Head-to-Tail Concatemers in Nuclei of Infected Cells and Their Role in the Generation of the Four Isomeric Arrangements of Viral DNA

Previous reports (H. Delius and J. B. Clements, J. Gen. Virol. 33:125-134, 1976; G. S. Hayward, R. J. Jacob, S. C. Wadsworth, and B. Roizman, Proc. Natl. Acad. Sci. U.S.A. 72:4243-4247, 1975; B. Roizman, G. S. Hayward, R. Jacob, S. W. Wadsworth, and R. W. Honess, Excerpta Med. Int. Congr. Ser. 2:188-198, 1974) have shown that herpes simplex virus DNA extracted from virions accumulating in the cytoplasm of infected cells consists of four populations of linear molecules differing in the orientation of the covalently linked large (L) and small (S) components relative to each other. Together, these four isomeric arrangements of viral DNA display four different termini and four different L-S component junctions. In the studies reported in this paper, we analyzed with restriction endonucleases the newly replicated viral DNA shortly after the onset of viral DNA synthesis, the progeny DNA accumulating in the nuclei late in infection, and rapidly sedimenting DNA present in nuclei of infected cells at 8 h after infection. In each instance the nuclear viral DNA contained a decreased concentration of all four terminal fragments and an increase in the concentration of fragments spanning the junction of L and S components relative to the concentration of other DNA fragments. The results are consistent with the hypothesis that the viral DNA accumulating in the nuclei consists of head-to-tail concatemers arising from the replication of DNA by a rolling-circle mechanism. A model is presented for generation of all four isomeric arrangements of herpes simplex virus DNA from one arrangement based on excision and repair of unit length DNA from head-to-tail concatemers and known features of the sequence arrangement of viral DNA.
A periodic state exchange protocol and its verification

We present an elegant protocol for reliably transmitting data messages from a sender to a receiver over a highspeed network that may reorder, lose, or corrupt messages. The protocol is based on a new principle that calls for the periodic exchange of state information between the sender and receiver. Our formal definition of the protocol is abstract and does not include explicit timing information such as the rate of sending state information. The abstract definition makes our formal verification of the protocol simple and based solely on well-established concepts: invariants, well-foundedness, and action fairness. We use the formal definition of the protocol and its proof of correctness to deduce the required timing information. In particular, we show that the rate of sending state information is at most (m-1)/2T where m is a measure of the memory size in the sender, and T is an upper bound on the required time for one message to be sent, propagated, and received between the sender and receiver. >
Glaucoma classification with a fusion of segmentation and image-based features

Automated classification of glaucoma is of interest in early detection and treatment. Existing methods employ features which are either image-based or derived from Optic Disc (OD) and Cup (OC) segmentation. While the latter suffers from segmentation inaccuracies, the image-based features tend to overfit in limited availability of training data. We propose a solution to overcome these issues and present a classification framework that fuses both type of features within a co-training based semi-supervised setting to overcome the paucity of labelled data. A novel set of features is proposed to represent the segmented OD-OC regions. Additionally, features based on Texture of projections and color Bag of Visual Words have been designed to be sensitive to the sector-wise deformations in OD. The proposed method was trained on 386 labelled and 717 unlabelled images. It outperformed existing methods with an accuracy and AUC of 73.28%, 0.79 on a private test set of 696 unseen images and 76.77%, 0.78 when cross-tested on DRISHTI-GS1 dataset.
Activation of the Behavioral Immune System: Putting the Brakes on Affiliation

Evolutionary psychologists propose that humans evolved a first line of defense against pathogens: the behavioral immune system (BIS). The BIS is thought to be functionally flexible such that the likelihood and magnitude of BIS activation depends on the individual’s perceived vulnerability to disease (PVD). Because conspecifics are sources of infection, the BIS has implications for affiliation. By priming and measuring chronic levels of PVD, we examined PVD’s relation to affiliation in zero-acquaintance situations in the laboratory, online, and during speed-dating events. Elevated BIS activation was associated with decreased attraction and affiliative behavior in situations that varied in the trade-off between social reward and potential risk of infection. These results were not due to attachment style, personality traits, or disgust sensitivity. This suggests that in social interactions, approach motivation associated with the need to belong may be weighed against avoidance motivation associated with the need to protect the self from disease.
A qualidade das informações de cor ou raça na RAIS: um estudo comparativo com o censo demográfico de 2010

Compara os dados da Relacao Anual de Informacoes Sociais (RAIS), do Ministerio do Trabalho e Emprego (MTE) e do Censo Demografico de 2010, do Instituto Brasileiro de Geografia e Estatistica (IBGE) de modo a identificar a presenca de diferencas significativas na maneira como estas fontes de dados capturam a informacao de cor ou raca dos trabalhadores, bem como a desigualdade salarial associada a esta variavel. Executa-se uma revisao do tema, identificando como tracos caracteristicos das diferencas metodologicas – isto e, de heteroatribuicao e autoatribuicao de pertenca racial – a tendencia do primeiro de superestimar a populacao branca e a subestimar magnitude da discriminacao racial. A analise dos dados verifica a presenca de superestimacao da populacao branca em algumas das regioes geograficas, mas nao verifica maior discriminacao racial na RAIS em relacao ao Censo demografico. Os modelos econometricos utilizados comprovam diferencas estatisticamente significativas na captura da desigualdade racial entre as duas pesquisas, alem de diferencas em termos de produtividade associadas as variaveis educacionais.
Alterations of high-mannose type N-glycosylation in human and mouse osteoarthritis cartilage.

OBJECTIVE The process of N-glycosylation is involved in the pathogenesis of various diseases. However, little is known about the contribution of changes in N-glycans in osteoarthritis (OA). The aim of this study was to identify the alterations in N-glycans in human OA cartilage, to characterize the messenger RNA (mRNA) expression of N-glycan biosynthesis enzyme genes (N-glycogenes) in mouse articular chondrocytes during cartilage degradation, and to analyze the relationship between altered N-glycan patterns and mechanisms of cartilage degradation. METHODS Alterations in N-glycans were analyzed in human OA cartilage and degraded mouse cartilage by high-performance liquid chromatography and mass spectrometry. N-glycogene mRNA expression in mouse chondrocytes was measured using reverse transcription-polymerase chain reaction. To assess the relationship between the altered N-glycans and degradation of mouse cartilage, experiments involving either knockdown or overexpression of N-glycogenes were performed in mouse articular chondrocytes. RESULTS Alterations in high-mannose type N-glycans were observed in both human OA cartilage and degraded mouse cartilage. The expression of β1,2N-acetylglucosaminyltransferase I (GlcNAc-TI) mRNA, which converts high-mannose type N-glycans, was significantly increased in degraded mouse cartilage. Mouse chondrocytes with suppressed GlcNAc-TI expression had reduced levels of matrix metalloproteinase 13 (MMP-13) and ADAMTS-5 (aggrecanase 2) mRNA following stimulation with interleukin-1α (IL-1α). In contrast, mouse chondrocytes overexpressing GlcNAc-TI had increased levels of MMP-13 and ADAMTS-5 mRNA following stimulation with IL-1α. CONCLUSION These findings indicate that alterations in high-mannose type N-glycans and N-glycogenes in chondrocytes correlate with the release of MMP-13 and ADAMTS-5 during cartilage degradation. These findings suggest that N-glycans play a crucial role in the initiation and progression of OA.
Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

Identification of populations and management units is an essential step in the study of natural systems. Still, there is limited consensus regarding how to define populations and management units, and whether genetic methods allow for inference at the relevant spatial and temporal scale. Here, we present a novel approach, integrating genetic, life history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model‐ and distance‐based genetic clustering methods were used to determine the population genetic structure in harbour seals. Second, we used harbour seal demographic and life history data to conduct population viability analyses (PVAs) in the vortex simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (Molecular Ecology, 19, 2010, 3038) ‘population viability criterion’ for demographic independence. The genetic analyses revealed fine‐scale population structuring in southern Scandinavian harbour seals and pointed to the existence of several genetic units. The PVAs indicated that the census population size of each of these genetic units was sufficiently large for long‐term population viability, and hence that the units could be classified as demographically independent management units. Our study suggests that population genetic inference can offer the same degree of temporal and spatial resolution as ‘nongenetic’ methods and that the combined use of genetic data and PVAs constitutes a promising approach for delineating populations and management units.
Ophthalmologist knowledge of evidence-based medicine and clinical practice guideline recommendations

The use of clinical practice guidelines (CPGs) saves time and provides the highest level of evidence, allowing busy ophthalmologists to make the best clinical decisions in a short amount of time. The aim of this study is to evaluate Iranian ophthalmologists’ knowledge and attitudes toward evidence-based medicine (EBM), and knowledge of CPGs. We performed a cross-sectional survey during the Annual Congress of the Iranian Society of Ophthalmology (November 2011). We administered 2 questionnaires regarding ophthalmologists’ attitudes towards EBM and self-reported clinical practices to a self-selected sample of ophthalmologists who volunteered to be surveyed. We employed descriptive statistics and unadjusted associations to describe the results. Of 556 attendees, 100 ophthalmologists responded to the first questionnaire, and 60% of them answered the second questionnaire. Although 83% had heard about EBM, only 11% knew what EBM was. Ninety-five percent of respondents believed in evidence-based ophthalmology training. Few understood EBM terminology. More than 60% of ophthalmologists surveyed had no familiarity with the Cochrane Library, MDConsult or Turning Research Into Practice (TRIP databases. Of the ophthalmologists surveyed, 26% implemented guidelines for problem solving, and 59% utilised the internet for finding clinical guidelines. The mean proportions of correct response to evidence-based cataract and glaucoma management questions were 68 and 56, respectively. Iranian ophthalmologists had a fair to poor knowledge but good attitudes towards EBM. Improving evidence-based knowledge and attitudes may be a component of improving Iranian ophthalmologists’ clinical practices.
Mining erasable itemsets

In this paper, we introduce a new kind of mining problem — - mining erasable itemsets, which is de-rived from planning products of the manufacturing industry. For this problem, we first present the formal definition of mining erasable itemsets and discuss some basic properties of the problem. Based on our analyses, we propose an efficient algorithm, META, for mining erasable itemsets. For evaluating META algorithm, we built three synthetic product databases. The results of applying META algorithm to these synthetic databases show its effectiveness.
Amide proton transfer imaging of the human breast at 7T: development and reproducibility

Chemical exchange saturation transfer (CEST) can offer information about protons associated with mobile proteins through the amide proton transfer (APT) effect, which has been shown to discriminate tumor from healthy tissue and, more recently, has been suggested as a prognosticator of response to therapy. Despite this promise, APT effects are small (only a few percent of the total signal), and APT imaging is often prone to artifacts resulting from system instability. Here we present a procedure that enables the detection of APT effects in the human breast at 7T while mitigating these issues. Adequate signal‐to‐noise ratio (SNR) was achieved via an optimized quadrature RF breast coil and 3D acquisitions. To reduce the influence of fat, effective fat suppression schemes were developed that did not degrade SNR. To reduce the levels of ghosting artifacts, dummy scans have been integrated into the scanning protocol. Compared with results obtained at 3T, the standard deviation of the measured APT effect was reduced by a factor of four at 7T, allowing for the detection of APT effects with a standard deviation of 1% in the human breast at 7T. Together, these results demonstrate that the APT effect can be reliably detected in the healthy human breast with a high level of precision at 7T. Copyright © 2013 John Wiley & Sons, Ltd.