Miracle-dz/UniFAR-FTUs huggingface dataset:
Cervical-type squamous metaplasia and myoepithelial cell differentiation in stromal tumor of the prostate.

REFERENCES 1. Agaram NP, Laquaglia MP, Ustun B, et al. Molecular characterization of pediatric gastrointestinal stromal tumors. Clin Cancer Res. 2008;14:3204–3215. 2. Astolfi A, Nannini M, Pantaleo MA, et al. A molecular portrait of gastrointestinal stromal tumors: an integrative analysis of gene expression profiling and high-resolution genomic copy number. Lab Invest. 2010;90:1285–1294. 3. Burnichon N, Brière JJ, Libé R, et al. SDHA is a tumor suppressor gene causing paraganglioma. Hum Mol Genet. 2010;19: 3011–3020. 4. Janeway KA, Zhu MJ, Barretina J, et al. Strong expression of IGF1R in pediatric gastrointestinal stromal tumors without IGF1R genomic amplification. Int J Cancer. 2010;127:2718–2722. 5. Janeway KA, Kim SY, Lodish M, et al. Defects in succinate dehydrogenase in gastrointestinal stromal tumors lacking KIT and PDGFRA mutations. Proc Natl Acad Sci U S A. 2011;108:314–318. 6. Marston Linehan W, Srinivasan R, Schmidt LS. The genetic basis of kidney cancer: a metabolic disease. Nature. 2010;7:277–285. 7. Pantaleo MA, Astolfi A, Di Battista M, et al. Insulin-like growth factor 1 receptor (IGF1r) expression in wild-type GIST: a potential novel therapeutic target. Int J Cancer. 2009; 125:2991–2994. 8. Pantaleo MA, Astolfi A, Indio V, et al. SDHA loss-of-function mutations in KITPDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst. 2011;103: 983–987. 9. Pasini B, McWhinney SR, Bei T, et al. Clinical and molecular genetics of patients with the Carney-Stratakis syndrome and germline mutations of the genes coding for the succinate dehydrogenase subunits SDHB, SDHC, and SDHD. Eur J Hum Genet. 2008;16:79–88. 10. Pasini B, Stratakis CA. SDH mutations in tumorigenesis and inherited endocrine tumours: lesson from the phaeochromocytoma-paraganglioma syndromes. J Int Med. 2009;266:19–42. 11. Rege TA, Wagner AJ, Corless CL, et al. “Pediatric-type” gastrointestinal stromal tumors in adults: distinctive histology predicts genotype and clinical behavior. Am J Surg Pathol. 2011;35:495–504. 12. Stratakis CA, Carney JA. The triad of parangangliomas, gastric stromal tumors and pulmonary chondromas (Carney triad), and the dyad of parangangliomas and gastric striomal sarcomas (CarneyStratakis syndrome): a molecular genetics and clinical implications. J Internal Med. 2009;266:43–52. 13. Tarn C, Rink L, Merkel E, et al. Insulinlike growth factor 1 receptor is a potential therapeutic target for gastrointestinal stromal tumors. Proc Natl Acad Sci USA. 2008;105:8387–8392.
Association between transforming growth factor beta1 gene polymorphisms and IgA nephropathy.

BACKGROUND Transforming growth factor beta1 (TGF-beta1) plays an important role in the modulation of cellular growth and differentiation in a wide variety of cell types and in the production/degradation of the extracellular matrix (ECM). We investigated whether G-800A, C-509T and Leu10-->Pro polymorphisms in the TGF-beta1 gene could be involved in the development and progression of immunoglobulin A nephropathy (IgAN). METHODS DNA samples were obtained from 101 patients with biopsy proven IgA mesangial nephropathy and 118 healthy controls. The genotypes of G-800A, C-509T and Leu10-->Pro polymorphisms in the TGF-beta1 gene were determined by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) with MaeIII, Eco 81I and Pst I, respectively. RESULTS No significant differences were observed in the genotype distribution of the three TGF-beta1 polymorphisms between patients and controls. The TAC haplotype (T=Leu10, A-800 and C-509 alleles, respectively) was significantly associated with IgAN (p=0.043; odds ratio (OR) =2.334, 95 % confidence interval (95%CI) 1.01-5.41). CONCLUSION Our study suggests that the haplotype reconstruction of TGF-beta1 gene polymorphisms could be more informative than the investigation of single nucleotide polymorphisms for defining the associated risk of developing IgAN. Further research is needed on larger cohorts to confirm TGF-beta1 involvement and test other TGF-beta1 variants with possible additive or synergistic effects.
Comparison of Salmonellaenterica Serovar Typhimurium Colitis in Germfree Mice and Mice Pretreated with Streptomycin

ABSTRACT Salmonella enterica subspecies 1 serovar Typhimurium is a common cause of bacterial enterocolitis. Mice are generally protected from Salmonella serovar Typhimurium colonization and enterocolitis by their resident intestinal microflora. This phenomenon is called “colonization resistance” (CR). Two murine Salmonella serovar Typhimurium infection models are based on the neutralization of CR: (i) in specific-pathogen-free mice pretreated with streptomycin (StrSPF mice) antibiotics disrupt the intestinal microflora; and (ii) germfree (GF) mice are raised without any intestinal microflora, but their intestines show distinct physiologic and immunologic characteristics. It has been unclear whether the same pathogenetic mechanisms trigger Salmonella serovar Typhimurium colitis in GF and StrSPF mice. In this study, we compared the two colitis models. In both of the models Salmonella serovar Typhimurium efficiently colonized the large intestine and triggered cecum and colon inflammation starting 8 h postinfection. The type III secretion system encoded in Salmonella pathogenicity island 1 was essential in both disease models. Thus, Salmonella serovar Typhimurium colitis is triggered by similar pathogenetic mechanisms in StrSPF and GF mice. This is remarkable considering the distinct physiological properties of the GF mouse gut. One obvious difference was more pronounced damage and reduced regenerative response of the cecal epithelium in GF mice. Overall, StrSPF mice and GF mice provide similar but not identical models for Salmonella serovar Typhimurium colitis.
Serum TK levels in CLL identify Binet stage A patients within biologically defined prognostic subgroups most likely to undergo disease progression

Abstract: Objective: Serum thymidine kinase (TK) levels have been shown to be correlated with survival in many malignancies, including chronic lymphocytic leukaemia (CLL). This study was designed to investigate associations between TK levels and other prognostic markers, in newly and previously diagnosed Binet stage A patients. Furthermore, the use of serum TK measurement to identify subcategories of disease within those defined by IgVH mutational status, gene usage and chromosomal aberrations was investigated. Methods: Ninety‐one CLL patients were enrolled. Serum TK levels were measured using a radioenzyme assay. IgVH mutational status and VH gene usage were determined using BIOMED‐2 primers and protocol. Recurring chromosomal abnormalities were detected by interphase fluorescent in situ hybridisation (FISH). Flow cytometry and reverse transcriptase polymerase chain reaction (RT‐PCR) determined CD38 and Zap‐70 expression, respectively. Results: Significantly higher serum TK levels were found in IgVH unmutated, compared with IgVH mutated, patients (P < 0.001). Elevated TK levels were also found in patients with CD38 and Zap‐70 positivity (P = 0.004, P < 0.001, respectively), short lymphocyte doubling time (LDT) (P = 0.044) and poor or intermediate prognosis chromosomal aberrations (P < 0.001). Conclusion: A TK level of >8.5 U/L best identified patients with progressive disease. Elevated TK levels could identify patients categorised, at diagnosis, into good prognosis subgroups by the various biological markers (mutated IgVH, good prognosis chromosomal aberrations, Zap‐70− and CD38−) who subsequently showed disease progression. Additionally, patients with VH3‐21 gene usage showed high TK levels, irrespective of mutational status, and serum TK measurement retained predictive power as disease progressed in all subcategories studied.
Women's labour contribution to productivity and efficiency in agriculture: empirical evidence from Bangladesh.

"This article examines the contribution of women's labour input to productivity and efficiency in crop farming using a large survey dataset of 1,839 households from 16 villages in two agro-ecological regions of Bangladesh. Results reveal that female labour accounts for a substantial 28% of total labour use (mainly supplied from the family) and contributes significantly to productivity as well as technical efficiency. Contrary to expectation, the cost share of female labour input is significantly higher than the male share, and has a substitution relationship with all other inputs, including male labour. The estimated mean level of technical efficiency is 0.90, implying that crop output might be increased by 10% by eliminating technical inefficiency. Both male and female education have a significant impact on improving technical efficiency. Other significant technical efficiency shifters are farming experience, family size and crop diversification. Owner operators are found to be technically inefficient relative to the tenants. Policy implications include creation of a hired labour market for female labour so that more women can be involved in the production process, and can contribute to towards improving productivity and efficiency. In addition, investment in education for both men and women, strategies to promote crop diversification and effective regulation/modification of the tenancy market will significantly improve technical efficiency in this case. " Copyright (c) 2010 The Author. Journal compilation (c) 2010 The Agricultural Economics Society.
Firm Adjustment to Trade Policy Changes in East Asia

Trade and investment liberalization has been one of the key features of economic policy in many developing countries since the 1990s. Research on this subject has consistently produced more evidence on the benefits of globalization; theoretical studies give more attention to what happens within an industry when trade and liberalization occur, while empirical studies confirm the positive impact of trade liberalization. We review some recent studies on the subject of firms in a globalized economy to enable us to understand more about how firms respond to globalization or changes in trade and investment liberalization. We focus on presenting or explaining the underlying mechanisms through which the effects are realized. The studies we summarized generally confirm the positive impact of trade liberalization on productivity or the spectrum of measures reflecting productivity, such as product quality, firm size, or skill intensity. The positive impact goes through various channels, including competition and industry dynamics, exporting and innovation decisions, and production or investment decisions.
Effect of replacement of soybean meal with Leucaena leucocephala leaf meal on performance, haematology, carcass measures and organ weight in broiler chickens.

This study was carried out to determine the effect of replacing soybean meal (SBM) with Leucaena leucocephala leaf meal (LLM) in the diet of broiler chickens. One hundred and fifty one-day-old broiler chicks were allotted to five treatments, each with three replicates and ten birds per replicate in a completely randomized design. The experiment was carried out at the University Teaching and Research Farm, Federal University of Technology Akure. The feeding trial lasted for 8 weeks. The treatments were Diet 1 (control, without LLM replacement) and Diets 2, 3, 4, and 5 where soybean meal (SBM) was replaced by 25%, 50%, 75%, and 100% of LLM, respectively from 0-56 days of rearing. Substitution of SBM with LLM significantly (P < 0.05) influenced the performance of broilers Original Research Article Eichie et al.; AJEA, 8(5): 327-334, 2015; Article no.AJEA. 2015.176 328 from day 0-28, but not at 29-56 days. Body weight gain of 907 g was obtained in birds on Diet 3 (50% LLM), while the least value of 553 g was obtained for Diet 5 with 100% LLM. The diet containing 50% LLM had better FCR (2.66) than the other treatments. Substitution of SBM with LLM did not significantly influence the haematological parameters except Erythrocyte Sedimentation Rate (ESR) concentration, which was significantly (P < 0.05) affected. Organ weights were not affected by diet from 0-28 days but from 29-56 days, weights of organs were significantly (P < 0.05) reduced as the level of LLM in diet increased. Carcass parts were significantly (P < 0.05) reduced by dietary LLM at 0-28 and 29-56 days, except for the back, drumstick, neck, head and shank that were not affected by LLM. Results of the study showed that LLM could be used to supplement SBM up to 50% in the diets of broiler chickens to improve performance and without adverse effect on the birds.
Neoadjuvant chemotherapy compared with surgery alone for locally advanced cancer of the stomach and cardia: European Organisation for Research and Treatment of Cancer randomized trial 40954.

PURPOSE Patients with locally advanced gastric cancer benefit from combined pre- and postoperative chemotherapy, although fewer than 50% could receive postoperative chemotherapy. We examined the value of purely preoperative chemotherapy in a phase III trial with strict preoperative staging and surgical resection guidelines. PATIENTS AND METHODS Patients with locally advanced adenocarcinoma of the stomach or esophagogastric junction (AEG II and III) were randomly assigned to preoperative chemotherapy followed by surgery or to surgery alone. To detect with 80% power an improvement in median survival from 17 months with surgery alone to 24 months with neoadjuvant, 282 events were required. RESULTS This trial was stopped for poor accrual after 144 patients were randomly assigned (72:72); 52.8% patients had tumors located in the proximal third of the stomach, including AEG type II and III. The International Union Against Cancer R0 resection rate was 81.9% after neoadjuvant chemotherapy as compared with 66.7% with surgery alone (P = .036). The surgery-only group had more lymph node metastases than the neoadjuvant group (76.5% v 61.4%; P = .018). Postoperative complications were more frequent in the neoadjuvant arm (27.1% v 16.2%; P = .09). After a median follow-up of 4.4 years and 67 deaths, a survival benefit could not be shown (hazard ratio, 0.84; 95% CI, 0.52 to 1.35; P = .466). CONCLUSION This trial showed a significantly increased R0 resection rate but failed to demonstrate a survival benefit. Possible explanations are low statistical power, a high rate of proximal gastric cancer including AEG and/or a better outcome than expected after radical surgery alone due to the high quality of surgery with resections of regional lymph nodes outside the perigastic area (celiac trunc, hepatic ligament, lymph node at a. lienalis; D2).
Voice-based Data Exploration : Chatting with your Database

Recent advances in automatic speech recognition and natural language processing have led to a new generation of robust voice-based interfaces. Yet, there is very little work on using voice-based interfaces to query database systems. In fact, one might even wonder who in her right mind would want to query a database system using voice commands! With this paper, we make the case for querying database systems using a voice-based interface, a new querying and interaction paradigm we call Query-by-Voice (QbV ). We will show the practicality and utility of QbV for relational DBMSs using a using a proof-ofconcept system called EchoQuery. There exists already work for building natural language interfaces for databases. A first major difference to this line of work is, that we use recent deep-learning models to allow for a robust translation from natural language to SQL. Another major difference from existing work is that the query interface of EchoQuery is inspired by regular human-to-human conversations in order to be natural for the user. ACM Reference Format: Prasetya Utama, Nathaniel Weir, Carsten Binnig, and Ugur Çetintemel. 2017. Voice-based Data Exploration: Chatting with your Database. In Proceedings of SCAI’17 . ACM, New York, NY, USA, 6 pages.
Handwritten and Machine-Printed Text Discrimination Using a Template Matching Approach

We propose a novel template matching approach for the discrimination of handwritten and machine-printed text. We first pre-process the scanned document images by performing denoising, circles/lines exclusion and word-block level segmentation. We then align and match characters in a flexible sized gallery with the segmented regions, using parallelised normalised cross-correlation. The experimental results over the Pattern Recognition & Image Analysis Research Lab-Natural History Museum (PRImA-NHM) dataset show remarkably high robustness of the algorithm in classifying cluttered, occluded and noisy samples, in addition to those with significant high missing data. The algorithm, which gives 84.0% classification rate with false positive rate 0.16 over the dataset, does not require training samples and generates compelling results as opposed to the training-based approaches, which have used the same benchmark.
Studies on the mechanism of the antimicrobial action of oleuropein.

Summary: Oleuropein, the bitter principle of green olives, is surface active; this and its effect on cell membranes, as demonstrated with human erythrocytes, seems to be the basis of its antimicrobial activity. Oleuropein effected a significant leakage of glutamate, potassium and inorganic phosphate from Lactobacillus plantarum. Oleuropein had no effect on the rate of glycolysis when added to resting cells of L. plantarum but it caused a decrease in the ATP content of the cells.
FERTILIZING ABILITY OF DILUTED RABBIT SEMEN ADDED WITH BEE POLLEN AQUEOUS EXTRACT

A total number of 221 New-Zealand White rabbits (45 sexually mature bucks aged 9 months, and 176 non-parous does aged 6 months) was used in 3 experiments. In experiment 1, semen was collected artificially, pooled and diluted with sodium chloride diluents (NaCl, 0.9%). Aqueous extracts of Bee-Pollen were added to the diluted semen at levels 0, 50, 100, or 150 μl/ ml, then the diluted semen was stored at refrigeration temperature (4-6C) for up to 3 days or incubated at 37C for up to 4 hours. Percentages of sperm motility; dead & abnormal spermatozoa and acrosomal damages were recorded at the different stages of the preservation. Experiment 2 was designed to evaluate the effect of Bee-Pollen aqueous extract on semen contamination with some bacteria present in diluted rabbit semen. In experiment 3, rabbit does were artificially inseminated using either the diluted semen free (control) or added with 100 μl Bee-Pollen extract/1 ml diluted semen (the level which showed the best effect on semen quality in experiment (1) to estimate the fertility traits. It was shown that, supplementing Bee-Pollen extract to the diluted rabbit semen significantly (P≤0.05) improved the sperm motility, while dead spermatozoa, sperm abnormalities and acrosomal damage percentages were significantly (P≤0.05) decreased, during storage at refrigeration temperature (4-6C) for up to 3 days or incubation at 37C for up to 4 hours. Semen quality and storageability (%) were arranged discendingly as obtained by added diluted semen with 150, 100, 50 μl Bee-Pollen extract/ ml than control. Semen quality decreased significantly (P≤0.05) with progression of time at different preservation temperatures. Aqueous extracts of Bee-Pollen at 150 and 100 μl/ml showed a better inhibitory effect on the microbial count compared with 50 and 0 μl Bee-Pollen/ml diluted semen.
Dietary consumption of Echinacea by mice afflicted with autoimmune (type I) diabetes: Effect of consuming the herb on hemopoietic and immune cell dynamics

Epidemiological studies indicate that the incidence of Type 1 diabetes, an autoimmune disease, is rising rapidly. However, none of the current therapies produces life long remission, or can prevent the disease onset. The NOD (non-obese diabetic) mouse is currently regarded as an excellent animal model of human Type 1 diabetes. NKT cells are known to be fundamental in modulating the disease, yet they are numerically and functionally deficient in mammals bearing this disease. Indeed, the role of NK cells in inhibiting autoimmunity in general is well established. Immunoregulatory strategies are currently believed to be the way of the future with respect to modulating autoimmune diseases. Based on this hypothesis, and the fact that the herb, Echinacea, is a well demonstrated immunostimulant of NK cells in normal mice/humans, we aimed to investigate, in NOD mice, the effect of short term (days) and long term (months) daily dietary administration of Echinacea, on the absolute levels of NK cells, and five other classes of hemopoietic and immune cells, in the bone marrow and spleen. The results revealed that, in NOD mice, dietary Echinacea, resulted in a significant increase in the absolute numbers of NK cells, irrespective of feeding duration, in the spleen, and moreover, it actually stimulated NK cell production in their bone marrow birth site. We further found that there were transient, early (days), herb exposure-time-dependent, quantitative changes in several of the other hemopoietic and immune cells populations in both the bone marrow and spleen. We conclude that consumption of this herb by NOD mice, at least, has lead to no negative repercussions with respect to the hemopoietic and immune lineages, and secondly, the consistent, long-lasting immunostimulation only of NK cells, may lead to a possible new approach to the treatment of Type 1 diabetes.
Does highly active antiretroviral therapy improve neurocognitive function? A systematic review

Highly active antiretroviral therapy (HAART) reduces the incidence of human immunodeficiency virus (HIV) dementia (HAD), whereas the overall prevalence appears to have increased. Recent changes to diagnostic nosology have emphasized the presence of neurocognitive deficits. Uniform methods of ascertaining neuropsychological impairment and excluding confounding causes are critical to between-study comparison. We conducted a systematic review on all studies that use single-cohort prospective treatment effect design that reported on the neurocognitive or neuropsychological profile of individuals commencing HAART. Fifteen 15 relevant studies were included. A large number of studies using observational or cross-sectional designs were excluded, as these do not allow for a within-subject description of pre- and post-HAART predictive factors. Eleven studies reported a significant improvement in neurocognitive status or neuropsychological profile over an average study period of 6 months. Variable or nonreporting of HAART regimens in these studies did not allow for an analysis of individual agent or regimen effectiveness. The results show that although HAART does improve cognition, it does not appear to fully eradicate impairments. The methods used in this research differ widely and therefore comparison across studies is difficult. Studies examining the long-term effects of HAART on HIV-associated neurocognitive disorders (HANDs) using uniform methods of data collection are needed, together with clear reporting of HAART regimens.
The multi-layer information bottleneck problem

The muti-layer information bottleneck (IB) problem, where information is propagated (or successively refined) from layer to layer, is considered. Based on information forwarded by the preceding layer, each stage of the network is required to preserve a certain level of relevance with regards to a specific hidden variable, quantified by the mutual information. The hidden variables and the source can be arbitrarily correlated. The optimal trade-off between rates of relevance and compression (or complexity) is obtained through a singleletter characterization, referred to as the rate-relevance region. Conditions of successive refinabilty are given. Binary source with BSC hidden variables and binary source with BSC/BEC mixed hidden variables are both proved to be successively refinable. We further extend our result to Guassian models. A counterexample of successive refinability is also provided.