Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence of Human Papillomavirus in Adolescent Girls Before Reported Sexual Debut

Background. Human papillomavirus (HPV) vaccines are recommended for girls prior to sexual debut because they are most effective if administered before girls acquire HPV. Little research has been done on HPV prevalence in girls who report not having passed sexual debut in high HPV-prevalence countries. Methods. Using attendance registers of randomly selected primary schools in the Mwanza region of Tanzania, we enrolled girls aged 15–16 years who reported not having passed sexual debut. A face-to-face interview on sexual behavior and intravaginal practices, and a nurse-assisted self-administered vaginal swab were performed. Swabs were tested for 13 high-risk and 24 low-risk HPV genotypes. Results. HPV was detected in 40/474 (8.4%; 95% confidence interval [CI], 5.9–11.0) girls. Ten different high-risk and 21 different low-risk genotypes were detected. High-risk genotypes were detected in 5.3% (95% CI, 3.5–7.8). In multivariable analysis, only intravaginal cleansing (practiced by 20.9%) was associated with HPV detection (adjusted odds ratio = 2.19, 95% CI, 1.09–4.39). Conclusion. This cohort of adolescent Tanzanian girls had a high HPV prevalence prior to self-reported sexual debut, and this was associated with intravaginal cleansing. This most likely reflects underreporting of sexual activity, and it is possible that intravaginal cleansing is a marker for unreported sexual debut or nonpenetrative sexual behaviors.
Phosphatidylserine dictates the assembly and dynamics of caveolae in the plasma membrane

Caveolae are bulb-shaped nanodomains of the plasma membrane that are enriched in cholesterol and sphingolipids. They have many physiological functions, including endocytic transport, mechanosensing, and regulation of membrane and lipid transport. Caveola formation relies on integral membrane proteins termed caveolins (Cavs) and the cavin family of peripheral proteins. Both protein families bind anionic phospholipids, but the precise roles of these lipids are unknown. Here, we studied the effects of phosphatidylserine (PtdSer), phosphatidylinositol 4-phosphate (PtdIns4P), and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) on caveolar formation and dynamics. Using live-cell, single-particle tracking of GFP-labeled Cav1 and ultrastructural analyses, we compared the effect of PtdSer disruption or phosphoinositide depletion with caveola disassembly caused by cavin1 loss. We found that PtdSer plays a crucial role in both caveola formation and stability. Sequestration or depletion of PtdSer decreased the number of detectable Cav1-GFP puncta and the number of caveolae visualized by electron microscopy. Under PtdSer-limiting conditions, the co-localization of Cav1 and cavin1 was diminished, and cavin1 degradation was increased. Using rapamycin-recruitable phosphatases, we also found that the acute depletion of PtdIns4P and PtdIns(4,5)P2 has minimal impact on caveola assembly but results in decreased lateral confinement. Finally, we show in a model of phospholipid scrambling, a feature of apoptotic cells, that caveola stability is acutely affected by the scrambling. We conclude that the predominant plasmalemmal anionic lipid PtdSer is essential for proper Cav clustering, caveola formation, and caveola dynamics and that membrane scrambling can perturb caveolar stability.
PAI-1 secretion and matrix deposition in human peritoneal mesothelial cell cultures: transcriptional regulation by TGF-beta 1.

BACKGROUND Plasminogen activator inhibitor-1 (PAI-1), the main inhibitor of plasminogen activators in plasma and in peritoneum, impairs plasmin formation that is essential for the repair processes of the mesothelium damaged by peritoneal dialysis fluids and peritonitis. The fibrogenetic cytokine transforming growth factor-beta (TGF-beta) displays variable effects on extracellular matrix remodeling enzymes and their inhibitors depending on tissues and cell lines. We previously found an unexpected stimulating effect of TGF-beta 1 on matrix metalloproteinase-9 in peritoneal mesothelial cells. In this study, we analyzed the effects of TGF-beta 1 on PAI-1 production and deposition in extracellular matrix. METHODS We used primary cultured mesothelial cells and a recently established human peritoneal mesothelial cell line (HMrSV5). Cell-associated and secreted plasminogen activators and their inhibitors were detected and characterized by substrate gel zymography. PAI-1 was identified by reverse zymography and by Western blotting, and total PAI-1 was measured by ELISA. Secreted and cell-associated PA activity was measured by its ability to activate plasminogen into plasmin, that is, by the release of paranitroaniline from the plasmin synthetic substrate S-2251. PAI-1 mRNA accumulation was assessed by Northern blot. In vitro nuclear run-on assays were carried out to determine whether TGF-beta 1 had transcriptional effects on PAI-1 expression. Finally, the subcellular distribution of PAI-1 was analyzed by immunofluorescence and by immunogold silver staining. RESULTS TGF-beta 1 increased PAI-1 antigen in the conditioned media of HMrSV5 cells, in a time- and concentration-dependent manner. This induced a dramatic decrease of free tPA in the cell medium and of membrane-bound uPA, and a parallel increase of high molecular weight PA-PAI complexes. Consequently, secreted and cell-associated plasminogen activator activities were considerably reduced. In primary cultured peritoneal mesothelial cells, TGF-beta 1 also induced PAI-1 secretion and the shift of tPA toward high molecular weight complexes. TGF-beta 1 increased PAI-1 mRNA in a time- and concentration-dependent manner. This effect was at least in part transcriptional since an approximately threefold increase in the rate of PAI-1 gene transcription was observed in nuclei sampled after a four-hour cell exposure to 5 ng/ml TGF-beta 1. Finally, TGF-beta 1 substantially increased the amount of intracellular and matrix-associated PAI-1. CONCLUSIONS These results suggest that excessive TGF-beta 1 stimulated PAI-1 could prevent appropriate peritoneal healing by impairing the degradation of fibrin and of unorganized matrix components, and by interfering with cell migration.
Unsupervised extraction of semantic relations using discourse information. (Extraction non supervisée de relations sémantiques par l'analyse du discours)

Natural language understanding often relies on common-sense reasoning, for which knowledge about semantic relations, especially between verbal predicates, may be required. This thesis addresses the challenge of using a distibutional method to automatically extract the necessary semantic information for common-sense inference. Typical associations between pairs of predicates and a targeted set of semantic relations (causal, temporal, similarity, opposition, part/whole) are extracted from large corpora, by exploiting the presence of discourse connectives which typically signal these semantic relations. In order to appraise these associations, we provide several significance measures inspired from the literature as well as a novel measure specifically designed to evaluate the strength of the link between the two predicates and the relation. The relevance of these measures is evaluated by computing their correlations with human judgments, based on a sample of verb pairs annotated in context. The application of this methodology to French and English corpora leads to the construction of a freely available resource, Lecsie (Linked Events Collection for Semantic Information Extraction), which consists of triples: pairs of event predicates associated with a relation; each triple is assigned significance scores based on our measures. From this resource, vector-based representations of pairs of predicates can be induced and used as lexical semantic features to build models for external applications. We assess the potential of these representations for several applications. Regarding discourse analysis, the tasks of predicting attachment of discourse units, as well as predicting the specific discourse relation linking them, are investigated. Using only features from our resource, we obtain significant improvements for both tasks in comparison to several baselines, including ones using other representations of the pairs of predicates. We also propose to define optimal sets of connectives better suited for large corpus applications by performing a dimension reduction in the space of the connectives, instead of using manually composed groups of connectives corresponding to predefined relations. Another promising application pursued in this thesis concerns relations between semantic frames (e.g. FrameNet): the resource can be used to enrich this sparse structure by providing candidate relations between verbal frames, based on associations between their verbs. These diverse applications aim to demonstrate the promising contributions provided by our approach, namely allowing the unsupervised extraction of typed semantic relations.
Thickness effect on the band gap and optical properties of germanium thin films

The band gap and optical properties (dielectric functions and optical constants) of Ge thin films with various thicknesses below 50 nm, which were synthesized with electron beam evaporation technique, have been determined using spectroscopic ellipsometry and UV-visible spectrophotometry. The optical properties are well described with the Forouhi–Bloomer model. Both the band gap and optical properties show a strong dependence on the film thickness. For film thickness smaller than ∼10 nm, a band gap expansion is observed as compared to bulk crystalline Ge, which is attributed to the one-dimensional quantum confinement effect. However, a band gap reduction was observed for thickness larger than ∼10 nm, which is explained in terms of the amorphous effect in the Ge layers.
Folate-conjugated amphiphilic block copolymer micelle for targeted and redox-responsive delivery of doxorubicin

Abstract In this paper, novel folate-conjugated and redox-responsive crosslinked block copolymer was successfully synthesized for targeted and controlled release of doxorubicin (DOX) to cancer cells. Folate-conjugated poly(ethylene glycol)-b-copolycarbonates (FA-PEG-b-P(MAC-co-DTC)) and methoxy poly(ethylene glycol)-b-copolycarbonates (mPEG-b-P(MAC-co-DTC)) were firstly synthesized by enzymatic method. FA-PEG/mPEG-b-P(MAC-co-DTC)-SS was then obtained by further crosslinking reaction with cystamine. Non-conjugated crosslinked copolymer mPEG-b-P(MAC-co-DTC)-SS- and non-conjugated uncrosslinked copolymer mPEG-b-P(MAC-co-DTC) were also synthesized for comparison. All the amphiphlic copolymers could self-assemble to form nano-sized micelles which dispersed in spherical shape before and after DOX loading. The core crosslinking structure of FA-PEG/mPEG-b-P(MAC-co-DTC)-SS could improve the micellar stability and drug loading capacity, while in vitro release studies also showed more sustained drug release behavior which could be accelerated in reductive condition. Moreover, confocal laser scanning microscopy indicated that the conjugation of FA could enhance the cellular uptake efficiency obviously via FA-receptor-mediated endocytosis, and MTT assays demonstrated highly potent cytotoxic activity of FA-PEG/mPEG-b-P(MAC-co-DTC)-SS.
Risk Factors in Domestic Homicides: Identifying Common Clusters in the Canadian Context

Little research has attempted to examine risk factor combinations when examining intimate partner violence. A variety of risk factors have been identified in domestic homicides, and it is recognized that risk of lethality may increase with the presence of more rather than less risk factors. This relationship is not necessarily linear, however. The objective of this study was to identify whether particular risk factor combinations are common in cases of domestic homicide. The study comprised 183 deaths that occurred between 2002 and 2012 and were reviewed by the Domestic Violence Death Review Committee, Office of the Chief Coroner of Ontario, Canada, with particular focus on the presence/absence of 40 empirically based risk factors. The analyses identified three distinct risk factor clusters that differed primarily by victim–perpetrator relationship and the likelihood of perpetrator suicide or attempts to commit suicide. Cases involving perpetrators currently in legal marriages or cohabitating with their victims were most common among the Non-Depressed/Non-Violent Cluster followed by the Depressed/Violent Cluster. In contrast, the majority of those in the Non-Depressed/Violent Cluster were estranged from their victims and the least likely to attempt/commit suicide. The study demonstrates that particular risk factor combinations are common in cases of domestic homicide. Future research should expand the number of risk factors examined, increase the sample size to further test cluster validity, and compare lethal and non-lethal intimate partner violence and homicide to allow for an examination of the clusters more unique to lethality. Prevention initiatives should emphasize the heterogeneity of domestic homicides and target specific interventions.
Impact of Weaning from Acute Dialytic Therapy on Outcomes of Chronic Kidney Disease following Urgent-Start Dialysis

Discontinuation of acute, unplanned dialysis is always an important therapeutic goal in dialysis-requiring patients with existing chronic kidney disease. Only a limited proportion of patients could be weaned off dialysis and remained dialysis-free. Here we performed a multicenter, observational study to investigate factors associated with successful weaning from acute dialysis, and to explore the potential impact of weaning itself on outcomes of patients with chronic kidney disease following urgent-start dialysis. We recruited 440 chronic kidney disease patients with a baseline estimated glomerular filtration rate <45 ml/min per 1/73 m2, and used propensity score-adjusted Cox regression analysis to measure the effect of weaning from acute dialysis on death during the index hospitalization and death or readmission after discharge. Over 2 years, 64 of 421 (15.2%) patients who survived >1 month died, and 36 (8.6%) were removed from dialysis, with 26 (6.2%) remaining alive and dialysis-free. Logistic regression analysis found that age ≧ 65 years, ischemic acute tubular necrosis, nephrotoxic exposure, urinary obstruction, and higher predialysis estimated glomerular filtration rate and serum hemoglobin were predictors of weaning off dialysis. After adjustment for propensity scores for dialysis weaning, Cox proportional hazards models showed successful weaning from dialysis (adjusted hazard ratio 0.06; 95% confidence interval 0.01 to 0.35), along with a history of hypertension and serum albumin, were independent protectors for early death. Conversely, a history of stroke, peripheral arterial disease and cancer predicted the occurrence of early mortality. In conclusion, this prospective cohort study shows that compared to patients with chronic kidney disease who became end-stage renal disease after acute dialysis, patients who could be weaned off acute dialytic therapy were associated with reduced risk of premature death over a 2-year observation period.
Chemical Composition and Insecticidal Activity of the Essential Oil of Illicium pachyphyllum Fruits against Two Grain Storage Insects

The aim of this research was to determine chemical composition and insecticidal activity of the essential oil of Illicium pachyphyllum fruits against two grain storage insects, Sitophilus zeamais and Tribolium castaneum, and to isolate any insecticidal constituents from the essential oil. The essential oil of I. pachyphyllum fruits was obtained by hydrodistillation and analyzed by GC-MS. A total of 36 components of the essential oil were identified, with the principal compounds in the essential oil being trans-ρ-mentha-1(7),8-dien-2-ol (24.56%), d-limonene (9.79%), caryophyllene oxide (9.32%), and cis-carveol (5.26%) followed by β-caryophyllene (4.63%) and bornyl acetate. Based on bioactivity-guided fractionation, the three active constituents were isolated and identified as trans-ρ-mentha-1(7),8-dien-2-ol, d-limonene and caryophyllene oxide. The essential oil of I. pachyphyllum fruits exhibited contact toxicity against S. zeamais and T. castaneum adults, with LD50 values of 17.33 μg/adult and 28.94 μg/adult, respectively. trans-p-Mentha-1(7),8-dien-2-ol (LD50 = 8.66 μg/adult and 13.66 μg/adult, respectively) exhibited stronger acute toxicity against S. zeamais and T. castaneum adults than either caryophyllene oxide (LD50 = 34.09 μg/adult and 45.56 μg/adult) and d-limonene (LD50 = 29.86 μg/adult and 20.14 μg/adult). The essential oil of I. pachyphyllum possessed fumigant toxicity against S. zeamais and T. castaneum adults with LC50 values of 11.49 mg/L and 15.08 mg/L, respectively. trans-p-Mentha-1(7),8-dien-2-ol exhibited stronger fumigant toxicity against S. zeamais and T. castaneum adults, respectively, with LC50 values of 6.01 mg/L and 8.14 mg/L, than caryophyllene oxide (LC50 = 17.02 mg/L and 15.98 mg/L) and d-limonene (LC50 = 33.71 mg/L and 21.24 mg/L). The results indicate that the essential oil of I. pachyphyllum fruits and its constituent compounds have potential for development into natural insecticides or fumigants for the control of insects in stored grains.
Graph Learning on K Nearest Neighbours for Automatic Image Annotation

Image annotation is an open and challenging task, especially with large label vocabulary. In this paper, we propose a novel graph learning based method for image annotation, which takes both advantages of the nearest neighbour based and the graph-based methods, by exploiting the graph learning method to propagate the labels on the graph corresponding to the K nearest neighbours of a test image. To acquire more effective graph weights for computing score for each label, besides the similarity of visual features, our method also considers the similarity of two label sets, which is computed based on the label correlation that captures the semantic information between two labels. In addition, we combine the image-to-label distance with the graph learning based score to compute the final decision value for labelling. The proposed method is evaluated on three benchmark datasets for image annotation. The result shows our method substantially outperforms the previous graph learning based methods, and our result matches the current state-of-the-art results in annotation quality.
Structure and specificity of lamprey monoclonal antibodies

Adaptive immunity in jawless vertebrates (lamprey and hagfish) is mediated by lymphocytes that undergo combinatorial assembly of leucine-rich repeat (LRR) gene segments to create a diverse repertoire of variable lymphocyte receptor (VLR) genes. Immunization with particulate antigens induces VLR-B-bearing lymphocytes to secrete antigen-specific VLR-B antibodies. Here, we describe the production of recombinant VLR-B antibodies specific for BclA, a major coat protein of Bacillus anthracis spores. The recombinant VLR-B antibodies possess 8–10 uniform subunits that collectively bind antigen with high avidity. Sequence analysis, mutagenesis, and modeling studies show that antigen binding involves residues in the β-sheets lining the VLR-B concave surface. EM visualization reveals tetrameric and pentameric molecules having a central core and highly flexible pairs of stalk-region “arms” with antigen-binding “hands. ” Remarkable antigen-binding specificity, avidity, and stability predict that these unusual LRR-based monoclonal antibodies will find many biomedical uses.
DELLA-Induced Early Transcriptional Changes during Etiolated Development in Arabidopsis thaliana

The hormones gibberellins (GAs) control a wide variety of processes in plants, including stress and developmental responses. This task largely relies on the activity of the DELLA proteins, nuclear-localized transcriptional regulators that do not seem to have DNA binding capacity. The identification of early target genes of DELLA action is key not only to understand how GAs regulate physiological responses, but also to get clues about the molecular mechanisms by which DELLAs regulate gene expression. Here, we have investigated the global, early transcriptional response triggered by the Arabidopsis DELLA protein GAI during skotomorphogenesis, a developmental program tightly regulated by GAs. Our results show that the induction of GAI activity has an almost immediate effect on gene expression. Although this transcriptional regulation is largely mediated by the PIFs and HY5 transcription factors based on target meta-analysis, additional evidence points to other transcription factors that would be directly involved in DELLA regulation of gene expression. First, we have identified cis elements recognized by Dofs and type-B ARRs among the sequences enriched in the promoters of GAI targets; and second, an enrichment in additional cis elements appeared when this analysis was extended to a dataset of early targets of the DELLA protein RGA: CArG boxes, bound by MADS-box proteins, and the E-box CACATG that links the activity of DELLAs to circadian transcriptional regulation. Finally, Gene Ontology analysis highlights the impact of DELLA regulation upon the homeostasis of the GA, auxin, and ethylene pathways, as well as upon pre-existing transcriptional networks.
Advances in mechanisms of resistance to aromatase inhibitors

Clinically, there are two distinct types of aromatase inhibitor (AI) resistance, namely acquired and innate resistance. Because the underlying mechanisms of these two types of resistance may not be mutually exclusive, strategies to tackle these resistances may not be effective when used interchangeably. Activation of growth factor receptor pathways is the hallmark of acquired AI resistance. These pathways can be targeted either at the cell surface receptor level or their downstream signaling cascades. Currently, everolimus in combination with exemestane represents a new standard of care for patients progressing on non-steroidal AIs. HDAC inhibitors have also shown promising results For innate resistance, the combination of fulvestrant and AI in the front line setting represents a new treatment option, particularly for patients who present with de novo metastatic disease. A Phase III trial is currently ongoing to evaluate the benefit of CDK 4/6 inhibitor, palbociclib, in the first line setting in combination with AI.