Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of drying temperature and final grain moisture content on the hulling and head rice yield efficiency of some common rough rice varieties

In drying process, drying temperature and final moisture content of grain are important factors that affect grain strength and consequently the waste of rice milling. In this research, effects of drying temperature in five levels (33, 38, 43, 48 and 53˚c) and ultimate moisture content of in five levels (8, 10, 12, 14 and 16% w.b.) on the milling waste of three common rice varieties in Gillan province includingand Ali Kazemi, Hashemi and Hasani. Laboratory oven were used for drying samples have been studyed.Initial seed moisture comtent was 24% w.b. Digital moisture content (model GMK-303) is used for determing grain moisture content.In this study were analyzed using completely randomized design with factorial experiment and to compare the means of main effects and interaction effects was used the duncans multiple range test was used. Milling of samples was performed by rubber roller huller and laboratory abrasive whiteing. Results of the data analysis showed that variety of Hasani (with average of 14.25%) had the minimum skinning waste among three mentioned varieties. Increasing of drying temperature (from 33 to 53˚c) increased average hulling waste significantly from 14.100 to 20.926%. On the other hand, increasing of moisture content of grain (from 8 to 16% w.b.) decreased significantly mean hulling waste from 22.016 to 14.605%. Moreover, in this study was determined that variety of Ali Kazemi had the minimum whiteing waste among three mentioned varieties. Increasing the ultimate moisture content of kernel and drying temperature affected significantly whiteing waste.With increasing drying temperature and reducing the final moisture content of grain amount of waste resulting from the mill in whiteing at significantly increased.
Activation of chronic toxoplasmosis by transportation stress in a mouse model

Toxoplasma gondiiis an obligate intracellular parasite infecting 25% of the world population and enormous number of animals. It can exist in two forms in intermediate hosts: the fast replicating tachyzoites responsible for acute infection and the slowly replicating bradyzoites responsible for life-long chronic infection. The interconversion between tachyzoites and bradyzoites plays critical roles in the transmission and pathogenesis of T. gondii. However, the molecular mechanisms that govern the interconversion are largely unknown. In this study, we established a chronic infection model in mice and examined the impact of transportation stress on the status of chronic infection. Our results demonstrated that, treating chronically infected mice with conditions mimicking transportation stress reduced the levels of several key cytokines that restrict the infection at chronic stage. Increased expression of the tachyzoite specific gene SAG1 (surface antigen 1) was detected in brain cysts of stress treated mice, indicating activation and conversion of bradyzoites to tachyzoites. Using this model, we identified fifteen toxoplasmic proteins that had significant abundance changes during stress induced cysts reactivation. These proteins serve as a basis for further investigation of the mechanisms governing bradyzoite conversion.
The CENP-T/-W complex is a binding partner of the histone chaperone FACT

Prendergast et al. identified Spt16 and SSRP1, subunits of the H2A–H2B histone chaperone FACT, as CENP-W-binding partners through a proteomic screen. They developed a model in which the FACT chaperone stabilizes the soluble CENP-T/-W complex in the cell and promotes dynamics of exchange, enabling CENP-T/-W deposition at centromeres.
Rivaroxaban dose adjustment using thrombin generation in severe congenital protein C deficiency and warfarin-induced skin necrosis.

Key Points Rivaroxaban was efficacious and safe in a child with protein C deficiency to prevent the recurrence of skin necrosis or venous thrombosis. The dosage of direct oral anticoagulants in children with thrombophilia is unclear; a thrombin generation assay may be useful to adjust it.
EGF induces epithelial-mesenchymal transition and cancer stem-like cell properties in human oral cancer cells via promoting Warburg effect

“Warburg effect”, the enhanced glycolysis or aerobic glycolysis, confers cancer cells the ability to survive and proliferate even under stressed conditions. In this study, we explored the role of epidermal growth factor (EGF) in orchestrating Warburg effect, the epithelial-mesenchymal transition (EMT) process, and the acquisition of cancer stem-like cell properties in human oral squamous cell carcinoma (OSCC) cells. Our results showed that EGF induces EMT process in OSCC cells, which correlates with the acquisition of cancer stem-like properties, including the enrichment of CD44+/CD24− population of cancer cells and an increased expression of CSC-related genes, aldehyde dehydrogenase-1 (ALDH1) and Bmi-1. We also showed that EGF concomitantly enhanced L-lactate production, while blocking glycolysis by 2-deoxy-D-glucose (2-DG) robustly reversed EGF-induced EMT process and CSC-like properties in OSCC cells. Mechanistically, we demonstrated that EGF promoted EMT process and CSC generation through EGFR/PI3K/HIF-1α axis-orchestrated glycolysis. Using an orthotopic tumor model of human OSCC (UM-SCC1) injected in the tongue of BALB/c nude mice, we showed that treatment with 2-DG in vivo significantly inhibited the metastasis of tumor cells to the regional cervical lymph nodes and reduced the expression of ALDH1 and vimentin in both in situ tumors and tumor cell-invaded regional lymph nodes. Taken together, these findings have unveiled a new mechanism that EGF drives OSCC metastasis through induction of EMT process and CSC generation, which is driven by an enhanced glycolytic metabolic program in OSCC cells.
Diagnostic quality of biopsy specimens: comparison between a conventional biopsy forceps and multibite forceps.

BACKGROUND The endoscopic biopsy is a prerequisite for histopathologic diagnosis. Various types of forceps are used to obtain tissue specimens. The aim of this study was to assess and compare the diagnostic quality of biopsy specimens obtained with a conventional forceps and a Multibite forceps. METHODS In a prospective, partially blinded, and randomized trial that included 250 patients referred for diagnostic upper and/or lower endoscopy, 510 biopsy specimens obtained with the Multibite forceps were compared with 520 specimens obtained with a conventional forceps. An experienced, blinded pathologist evaluated the specimens for diameter, depth of specimen, artifacts, anatomic orientation, vitality, general histologic quality, and diagnostic quality. Statistical analysis was performed by using the Fisher exact test. A p value of < 0.05 was regarded as significant. RESULTS There were no statistically significant differences between the specimens obtained with the 2 forceps. The p values for the evaluated parameters were as follows: diameter 0.45, depth of specimen 0.56, artifacts 1.0, pathoanatomic orientation 0.40, vitality 0.45, and histologic diagnostic quality 0.53. CONCLUSION The quality of biopsy specimens obtained with the Multibite forceps is comparable with that of specimens taken with a conventional forceps. Use of the Multibite forceps saves time in that 4 specimens can be obtained in 1 pass in situations in which a large number of specimens are needed or when the potential for transmission of infection is of concern.
Arabidopsis mRNA decay landscape arises from specialized RNA decay substrates, decapping-mediated feedback, and redundancy

Significance Gene expression is governed by the opposing forces of transcription and decay. How RNA decay modulates the transcriptome is largely unknown, including whether the three major cytoplasmic degradative pathways (mRNA decapping, the RNA exosome, and SOV/DIS3L2) act on specific sets of RNAs. We used maximum likelihood mathematical modeling and RNAseq to analyze mRNA decay in wild-type and Arabidopsis RNA decay mutants. We demonstrate that mRNA decapping contributes broadly to mRNA decay (68% of RNAs), and is especially important for short-lived RNAs. SOV deficiency caused slower decay of few transcripts, but also elicited broad feedback: Many RNAs decayed faster, and required mRNA decapping for this faster rate. Despite altered turnover, these RNAs were maintained at near-wild-type abundance. The decay of mRNA plays a vital role in modulating mRNA abundance, which, in turn, influences cellular and organismal processes. In plants and metazoans, three distinct pathways carry out the decay of most cytoplasmic mRNAs: The mRNA decapping complex, which requires the scaffold protein VARICOSE (VCS), removes a protective 5′ cap, allowing for 5′ to 3′ decay via EXORIBONUCLEASE4 (XRN4, XRN1 in metazoans and yeast), and both the exosome and SUPPRESSOR OF VCS (SOV)/DIS3L2 degrade RNAs in the 3′ to 5′ direction. However, the unique biological contributions of these three pathways, and whether they degrade specialized sets of transcripts, are unknown. In Arabidopsis, the participation of SOV in RNA homeostasis is also unclear, because Arabidopsis sov mutants have a normal phenotype. We carried out mRNA decay analyses in wild-type, sov, vcs, and vcs sov seedlings, and used a mathematical modeling approach to determine decay rates and quantify gene-specific contributions of VCS and SOV to decay. This analysis revealed that VCS (decapping) contributes to decay of 68% of the transcriptome, and, while it initiates degradation of mRNAs with a wide range of decay rates, it especially contributes to decay of short-lived RNAs. Only a few RNAs were clear SOV substrates in that they decayed more slowly in sov mutants. However, 4,506 RNAs showed VCS-dependent feedback in sov that modulated decay rates, and, by inference, transcription, to maintain RNA abundances, suggesting that these RNAs might also be SOV substrates. This feedback was shown to be independent of siRNA activity.
HIV and tuberculosis – science and implementation to turn the tide and reduce deaths

Every year, HIV‐associated tuberculosis (TB) deprives 350,000 mainly young people of productive and healthy lives. People die because TB is not diagnosed and treated in those with known HIV infection and HIV infection is not diagnosed in those with TB. Even in those in whom both HIV and TB are diagnosed and treated, this often happens far too late. These deficiencies can be addressed through the application of new scientific evidence and diagnostic tools.
Automatic Measurement of Thalamic Diameter in 2-D Fetal Ultrasound Brain Images Using Shape Prior Constrained Regularized Level Sets

We derived an automated algorithm for accurately measuring the thalamic diameter from 2-D fetal ultrasound (US) brain images. The algorithm overcomes the inherent limitations of the US image modality: nonuniform density; missing boundaries; and strong speckle noise. We introduced a “guitar” structure that represents the negative space surrounding the thalamic regions. The guitar acts as a landmark for deriving the widest points of the thalamus even when its boundaries are not identifiable. We augmented a generalized level-set framework with a shape prior and constraints derived from statistical shape models of the guitars; this framework was used to segment US images and measure the thalamic diameter. Our segmentation method achieved a higher mean Dice similarity coefficient, Hausdorff distance, specificity, and reduced contour leakage when compared to other well-established methods. The automatic thalamic diameter measurement had an interobserver variability of -0.56 ± 2.29 mm compared to manual measurement by an expert sonographer. Our method was capable of automatically estimating the thalamic diameter, with the measurement accuracy on par with clinical assessment. Our method can be used as part of computer-assisted screening tools that automatically measure the biometrics of the fetal thalamus; these biometrics are linked to neurodevelopmental outcomes.
Heterotypic paracrine signaling drives fibroblast senescence and tumor progression of large cell carcinoma of the lung

Senescence in cancer cells acts as a tumor suppressor, whereas in fibroblasts enhances tumor growth. Senescence has been reported in tumor associated fibroblasts (TAFs) from a growing list of cancer subtypes. However, the presence of senescent TAFs in lung cancer remains undefined. We examined senescence in TAFs from primary lung cancer and paired control fibroblasts from unaffected tissue in three major histologic subtypes: adenocarcinoma (ADC), squamous cell carcinoma (SCC) and large cell carcinoma (LCC). Three independent senescence markers (senescence-associated beta-galactosidase, permanent growth arrest and spreading) were consistently observed in cultured LCC-TAFs only, revealing a selective premature senescence. Intriguingly, SCC-TAFs exhibited a poor growth response in the absence of senescence markers, indicating a dysfunctional phenotype rather than senescence. Co-culturing normal fibroblasts with LCC (but not ADC or SCC) cancer cells was sufficient to render fibroblasts senescent through oxidative stress, indicating that senescence in LCC-TAFs is driven by heterotypic signaling. In addition, senescent fibroblasts provided selective growth and invasive advantages to LCC cells in culture compared to normal fibroblasts. Likewise, senescent fibroblasts enhanced tumor growth and lung dissemination of tumor cells when co-injected with LCC cells in nude mice beyond the effects induced by control fibroblasts. These results define the subtype-specific aberrant phenotypes of lung TAFs, thereby challenging the common assumption that lung TAFs are a heterogeneous myofibroblast-like cell population regardless of their subtype. Importantly, because LCC often distinguishes itself in the clinic by its aggressive nature, we argue that senescent TAFs may contribute to the selective aggressive behavior of LCC tumors.
Learning Role-based Graph Embeddings

Random walks are at the heart of many existing network embedding methods. However, such algorithms have many limitations that arise from the use of random walks, e.g., the features resulting from these methods are unable to transfer to new nodes and graphs as they are tied to vertex identity. In this work, we introduce the Role2Vec framework which uses the flexible notion of attributed random walks, and serves as a basis for generalizing existing methods such as DeepWalk, node2vec, and many others that leverage random walks. Our proposed framework enables these methods to be more widely applicable for both transductive and inductive learning as well as for use on graphs with attributes (if available). This is achieved by learning functions that generalize to new nodes and graphs. We show that our proposed framework is effective with an average AUC improvement of 16:55% while requiring on average 853x less space than existing methods on a variety of graphs.
Different cell sizes in human limbal and central corneal basal epithelia measured by confocal microscopy and flow cytometry.

PURPOSE In the epidermis, the highest clonogenicity, a feature of stem cells (SCs), is found in the smallest keratinocyte. In the limbal-corneal (LC) epithelium the SCs are exclusively localized in the basal epithelial layer of the limbal domain. The current study was conducted to determine whether this spatial SC arrangement is reflected in differences in the cell size between limbal and corneal cells. METHODS In vivo confocal microscopy was used to scan and measure the size of the cells of the central cornea and the superior limbus in five normal subjects, from the superficial to the basal cell layer. Limbal and corneal pure epithelial sheets were isolated by dispase digestion from human tissues and dissociated into single cells by trypsin digestion. The forward (FSC; a relative measure of cell size) and side (SSC; a relative measure of cytoplasmic complexity) light-scattering properties of these cells were determined by flow cytometry. RESULTS Confocal microscopy showed that diameters of the basal cells of the limbal and corneal zones were 10.1 +/- 0.8 and 17.1 +/- 0.8 micro m, respectively. The corresponding values for the superficial layers were 19.9 +/- 1.6 and 36.6 +/- 1.6 microm, respectively (P < 0.0001). The mean FSC and SSC of the limbal cells amounted to 65.7% +/- 8.7% and of the corneal cells, 74.4% +/- 4.6%. Furthermore, only 1.40% +/- 0.83% and 0.69% +/- 0.37% of the corneal cells had FSC and SSC equal to the lowest 15% of FSC and SCC of the limbal cells, respectively, indicating that the limbus contained a substantial proportion of very low FSC and SSC cells for which there was no corneal counterpart. CONCLUSIONS The data collectively demonstrate that the smallest cells are located in the limbal basal epithelium. This feature may help isolate corneal SCs located in the limbus.
DNMT3B in vitro knocking-down is able to reverse embryonal rhabdomyosarcoma cell phenotype through inhibition of proliferation and induction of myogenic differentiation

Aberrant DNA methylation has been frequently observed in many human cancers, including rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children. To date, the expression and function of the de novo DNA methyltransferase (DNMT) 3B in RMS have not yet been investigated. Our study show for the first time a significant up-regulation of DNMT3B levels in 14 RMS tumour samples and 4 RMS cell lines in comparison to normal skeletal muscle. Transfection of RD and TE671 cells, two in vitro models of embryonal RMS (ERMS), with a synthetic DNMT3B siRNA decreased cell proliferation by arresting cell cycle at G1 phase, as demonstrated by the reduced expression of Cyclin B1, Cyclin D1 and Cyclin E2, and by the concomitant up-regulation of the checkpoint regulators p21 and p27. DNMT3B depletion also impaired RB phosphorylation status and decreased migratory capacity and clonogenic potential. Interestingly, DNMT3B knock-down was able to commit ERMS cells towards myogenic terminal differentiation, as confirmed by the acquisition of a myogenic-like phenotype and by the increased expression of the myogenic markers MYOD1, Myogenin and MyHC. Finally, inhibition of MEK/ERK signalling by U0126 resulted in a reduction of DNMT3B protein, giving evidence that DNMT3B is a down-stream molecule of this oncogenic pathway. Taken together, our data indicate that altered expression of DNMT3B plays a key role in ERMS development since its silencing is able to reverse cell cancer phenotype by rescuing myogenic program. Epigenetic therapy, by targeting the DNA methylation machinery, may represent a novel therapeutic strategy against RMS.
Mechanically Fastened FRP-Strengthened Two-Way Concrete Slabs with and without Cutouts

The feasibility of strengthening concrete slabs in flexure, with and without cutouts, using the mechanically fastened MF FRP technique is investigated. Two series of large-scale reinforced concrete slabs are tested. The first series is comprised of five slabs without a cutout, and measuring 2,6002,600120 mm; the second series consists of four slabs of the same dimensions with a central cutout measuring 800800 mm. The mechanically fastened system is found to be a valid alternative to the externally bonded system resulting in a rapid, economic, and effective strengthening technique for two-way concrete slabs. The increases in ultimate capacities of the MF FRP-strengthened slabs range between 30 and 70% over those of the unstrengthened specimens. In addition, finite-element modeling of MF FRP-strengthened slabs is introduced in this study. The interfacial behavior between the MF FRPs and the concrete substrate is accounted for by using appropriate interfacial models. Very good agreement is obtained between the test results and the numerical predictions.
Characteristics of Age-Discordant Partnerships Associated With HIV Risk Among Young South African Women (HPTN 068)

Objective:Sexual liaisons between older men and younger women have been linked to greater risk of HIV acquisition. This study aims to (1) identify psychosocial and behavioral factors associated with age-discordant (partner ≥5 years) versus age-concordant partnerships (−1< partner <5) and (2) examine the association between partner age discordance and young South African women's sexual behavior. Methods:We used generalized estimating equations to analyze responses from 656 sexually experienced women (aged 13–20 years) from rural Mpumalanga province. Results:Partner age discordance was associated with greater odds of reporting both more frequent sex [adjusted odd ratio (aOR) = 1.77; 95% confidence interval (CI): 1.20 to 2.60] and having a partner with concurrent partnerships (aOR = 1.77; 95% CI: 1.22 to 2.57). Age-discordant partnerships were associated with greater odds of casual partnerships (aOR = 1.50; 95% CI: 1.06 to 2.13), having a partner with concurrent partnerships (aOR = 1.71; 95% CI: 1.19 to 2.46), and more frequent intercourse (ie, having sex at least 2 or 3 times per month) (aOR = 2.04; 95% CI: 1.39 to 3.00). They were associated with lower odds of reporting condom use at last sex (aOR = 0.70; 95% CI: 0.50 to 0.98) and always using condoms (aOR = 0.53; 95% CI: 0.32 to 0.88) in age-discordant partnerships. Conclusions:Our findings suggest that a history of age-discordant partnerships, and to a lesser extent having an age-discordant partner, is linked to HIV risk among young South African women; however, the link between partner age discordance and HIV risk may be more strongly related to the characteristics of age-discordant partnerships than to the characteristics of young women who form such partnerships.
The evolution of between‐species reproductive interference capability under different within‐species mating regimes

Sexual selection sometimes favors male traits that benefit their bearers, but harm their mates. The harmful effects of male traits may also extend to females of other species via heterospecific mating interactions. This could affect the coexistence of closely related species during secondary contact. We examined the evolution of the interspecific interfering capability of a beetle (Callosobruchus chinensis) with a congener (C. maculatus) using C. chinensis males reared under conditions of monogamy and polygamy for 17 generations. After experimental evolution, C. chinensis males reared under polygamous conditions imposed greater impacts on offspring production by C. maculatus females than did C. chinensis males reared under monogamous conditions. However, the mechanism by which differential mating regimes altered the effect of C. chinensis males on C. maculatus females was unclear, because we did not find evidence for the expected genital evolution in C. chinensis, despite their body size divergence. Our findings suggest that traits that originally evolved through sexual selection in two allopatric species could influence the coexistence of these species or the likelihood of reinforcement during secondary contact.