Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Pacific meridional mode on ENSO evolution and predictability: asymmetric modulation and ocean preconditioning

<p>This study investigates the mechanisms for the Pacific meridional mode (PMM) to influence the development of an ENSO event and its seasonal predictability. To examine the relative importance of several factors that might modulate the efficiency of the PMM influence, we conduct a series of prediction experiments to selected ENSO events with different intensity from a long simulation of the Community Earth System Model (CESM). Using the same coupled model, each of the ensemble prediction is conducted from slightly different ocean initial states but under a common prescribed PMM surface heat flux forcing. In general, the matched PMM forcing to ENSO, i.e., a positive (negative) PMM prior to an El Ni&#241;o (a La Ni&#241;a), plays an enhancing role while a mismatched PMM forcing plays a damping role. For the matched PMM-ENSO events, the positive PMM exerts greater influence than its negative counterpart does, with stronger enhancement of positive PMM events on an El Ni&#241;o than that of negative PMM events on a La Ni&#241;a. This asymmetry in ENSO influence largely originates from the intensity asymmetry between the positive and negative PMM events in the tropics, which can be explained by the nonlinearity in the growth and equatorward propagation of the PMM-related SST and surface zonal wind anomalies through both wind-evaporation-SST (WES) feedback and summer deep convection (SDC) response. Furthermore, the response of ENSO to an imposed PMM forcing is modulated by the preconditioning of the upper ocean heat content, which provides the memory for the coupled low-frequency evolution in the tropical Pacific. </p>
Crystallographic orientation dependence of mean etchable fission track length in apatite; an empirical model and experimental observations

Partially annealed thermal-neutron-induced fission tracks in apatite exhibit mean etchable lengths that range continuously between a maximum for tracks oriented parallel to the crystallographic c-axis and a minimum for tracks perpendicular to c. A simple empirical model quantifies this crystallographic orientation dependence based on the assumption that the mean etchable fission track length aL ary angle to the c-axis is given by the corresponding radius of an ellipse. The ellipse has semiaxes equal to, respectively, the mean track lengths parallel (/") and perpendicular (/.) to the c-axis. The elliptical model is tested against 6l isothermal partial annealing experiments performed on thermal-neutron-induced fission tracks in Tioga apatite. It is found to adequately characterize etchable fission track length distributions in partially annealed apatites when /. > 8.4 pm. The difference between l. and l^ increases systematically and continuously as both mean lengths decrease, and fission-track lengths are distributed normally about their mean with a standard deviation of ca. 0.75 pm, regardless of crystallographic orientation and relative degree of partial annealing. For /" < 8.4 pm, the elliptical model apparently fails because tracks at relatively high angles to the c-axis experience greatly accelerated etchable length reduction. Experimentally determined values of /" and /. in apatite have greater physical significance than does the arithmetic (conventional) mean fission track length. Application of the proposed elliptical annealing model to controlled laboratory experiments may provide valuable insight, heretofore unattainable, into the physical process(es) by which fission tracks anneal in apatite.
HER2 Testing for Breast Cancer in the Genomics Laboratory: A Sea Change for FISH.

CONTEXT. — Guidelines for HER2 testing in breast cancer have changed over time, from the US Food and Drug Administration guideline to the American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines published in 2007, 2013, and 2018. OBJECTIVE. — To investigate the change in assignment of HER2 status in breast cancers with equivocal (2+) immunohistochemistry (IHC) results by fluorescence in situ hybridization (FISH) following implementation of the ASCO/CAP 2018 guideline. DESIGN. — The study included 3556 invasive breast cancers that were HER2 equivocal (2+) by IHC and were submitted to our FISH laboratory after July 2018. Reflex testing (with repeat IHC staining) was performed on certain categories of FISH results known as groups 2, 3, and 4. Concomitant review of IHC and FISH was performed on these reflex cases per 2018 guideline recommendations. The FISH data were analyzed to compare US Food and Drug Administration and ASCO/CAP 2007, 2013, and 2018 interpretations. RESULTS. — Of 3548 invasive breast cancers with complete data available, the percentage agreement for FISH according to different guidelines was highest for ASCO/CAP 2018 versus US Food and Drug Administration (96.5%), followed by ASCO/CAP 2018 versus 2007 (93.8%), and lowest with ASCO/CAP 2018 versus 2013 (83.7%). Per the 2018 guideline, reflex IHC testing was performed on 633 breast cancers (17.8%); the majority of reflex testing results were negative (541 of 633; 85.5%). The overall distribution of HER2 FISH results (per the 2018 guideline) was 88.5% negative and 11.5% positive. CONCLUSIONS. — By eliminating the equivocal FISH category, the 2018 ASCO/CAP guideline significantly reduced the HER2 FISH-positive rate in tumors with equivocal (2+) IHC results.
Influence of Polyethylene Glycol on Leaf Anatomy, Stomatal Behavior, Water Loss, and Some Physiological Traits of Date Palm Plantlets Grown In Vitro and Ex Vitro

Few reports explain the mechanism of PEG action on stomatal behavior and anatomical structure and analyze the photosynthetic pigments of in vitro date palm plantlets for better tolerance to ex vitro exposure. The main challenge for in vitro micropropagation of date palm techniques remains restricted to high survival rates and vigorous growth after ex vitro transplantation. In vitro hardening is induced by Polyethylene glycol PEG (0.0, 10, 20, 30 g L−1) for 4 weeks. Leaf anatomy, stomatal behavior, water loss %, photosynthetic pigments, and reducing sugars were examined in date palm plantlets (Phoenix dactylifera L.) cv. (Sewi) after 4 weeks from in vitro PEG treatment and after 4 weeks from ex vitro transplanting to the greenhouse. Leaf anatomy and the surface ultrastructure of in vitro untreated leaves showed a thin cuticle layer, wide opened malfunctioning stomata, and abnormal leaf anatomy. Furthermore, addition of PEG resulted in increasing cuticle thickness, epicuticular wax depositions, and plastids density, improving the stomatal ability to close and decreasing the stomatal aperture length while reducing the substomatal chambers and intercellular spaces in the mesophyll. As a result, a significant reduction in water loss % was observed in both in vitro and ex vitro PEG treated leaves as compared to untreated ones, which exhibited rapid wilting when exposed to low humidity for 4 h. PEG application significantly increased Chlorophylls a, b and carotenoids concentrations, especially 10, 20 g L−1 treatments, which were sequentially reflected in increasing the reducing sugar concentration. However, leaves of plantlets treated with PEG at 30 g L−1 became yellow and had necrosis ends with death. In vitro hardening by 20 g L−1 PEG increased the survival rate of plantlets to 90% after ex vitro transfer compared to 63% recorded for the untreated plantlets. Therefore, this application provides normal date palm plantlets developed faster and enhances survival after ex vitro transfer.
Hashtag favela: Instagram, space and identity in urban Brazil

Instagram is a virtual, multi-authored platform that symbolizes geographic realities by allowing its users to capture time-and-space-specific characteristics through photographs or videos. As opposed to the selective reproduction of dominant discourses, Instagram users collaboratively produce multiple truths based on their own personal perceptions and experiences. Considering that favelas in Brazil are some of the most stigmatized, misrepresented and misunderstood places in the world, this article follows the term ‘favela’ (#favela) to better understand how it is being used by the masses in 2019. Ultimately, this article analyses the space and identity of ‘favelas’ in urban Brazil by dividing our findings into three separate categories: (1) ‘hashtag favela as advertising’, (2) ‘hashtag favela as tourism’ and (3) ‘hashtag favela as everyday’. We found that although Instagram promotes the ability of favela residents to represent themselves, #favela continues to be co-opted by outsiders. Interestingly, when the term is co-opted by outsiders, its meaning is transformed from a physical space or neighbourhood into one of the many types of commodities to be bought and sold.
Screening for Sodium-Salt Tolerance at the Seedling Stage of Rice (Oryza sativa L.) Genotypes from Sudan and South Sudan

Morpho-physiological and genetic studies of salinity are important in understanding the mechanism of plant adaptation to stressful environment. Eighteen rice genotypes collected from Sudan and South Sudan, which were never tested for salt tolerance, as well as two genotypes (FL478 as tolerant check and IR29 as sensitive check) from the International Rice Research Institute (IRRI), were subjected to salinity stress at seedling stage. Test was carried out in hydroponic system applying electrical conductivity (EC) 12 dS/m NaCl using randomized complete block design with three replicates. Most of the genotypes showed sensitivity to salt stress; one genotype PIPANFARY RED2 was moderately sensitive and three genotypes MASURY1, MASURY2 and FL478 were tolerant. Salinity significantly reduced leaf dry weight, shoot dry weight, root dry weigh and biomass production (biomass/plant) by 31%, 42%, 60% and 47%, respectively. Tolerant genotypes accumulated low amount (2.52 g/100 g dry weight (dwt)) of Na in the root, whereas highly sensitive genotypes accumulated high amount (3.87 g/100 g dwt) of Na. Tolerant genotypes showed less reduction in K concentration than the sensitive genotypes. Therefore, they maintained lowest Na/K ratio in the shoot (1.47%) than in the root (3.69%) compared to the intolerant genotypes (7.49% and 8.49%). The genotypes that showed tolerance to salinity stress can be used as a source of resistance/tolerance in a breeding program for rice improvement in uplands areas in semi-arid condition.
Nest structure and thermoregulation in the stingless bee Trigona (Plebeina) denoiti Vachal (Hymenoptera: Apidae)

Nests of the ground-nesting stingless bee Trigona (Plebeina) denoiti were excavated in Natal and compared with descriptionptions of nests excavated in Tanzania around 1953. A number of differences were found, among them a greater variation in the structure of the brood nest. Although the brood combs were spirally arranged, as in the Tanzanian nests, double as well as single spirals occurred and both types rotated either clockwise or anti-clockwise. The unique features of the nest architecture are discussed.
Measuring Technical Efficiency of Wheat Farms in Punjab, Pakistan: A Stochastic Frontier Analysis Approach

The wheat productivity in Punjab is less than the potential maximum due to imbalanced input use and farm management issues. Many studies have attemped to estimate technical efficiency of wheat crops using different techniques. However, most of them used limited datasets that focus on only a few districts. This study study uses a comprehensive dataset which is representive of Punjab province. We used farm-level panel survey data collected from 1581 farms in 17 districts of Punjab from 2005-06 to 2007-08. The technical efficiency of the wheat farms was analyzed using Stochastic Frontier Analysis (SFA) approach. Further, we identified the determinants of (in)efficiency using the same method. The results show that the mean technical efficiency of wheat farmers in Punjab is 84 percent indicating a considerable room for efficiency improvement. Further, the results indicate that technical efficiency could be improved by educating the younger farmers, building road infrastructure, and improving farmers’ access to essential inputs. The study supports the argument that wheat farmers are less technically efficient in Punjab, Pakistan.
Single-Cell Profiling of AKI in a Murine Model Reveals Novel Transcriptional Signatures, Profibrotic Phenotype, and Epithelial-to-Stromal Crosstalk.

BACKGROUND Current management of AKI, a potentially fatal disorder that can also initiate or exacerbate CKD, is merely supportive. Therefore, deeper understanding of the molecular pathways perturbed in AKI is needed to identify targets with potential to lead to improved treatment. METHODS We performed single-cell RNA sequencing (scRNA-seq) with the clinically relevant unilateral ischemia-reperfusion murine model of AKI at days 1, 2, 4, 7, 11, and 14 after AKI onset. Using real-time quantitative PCR, immunofluorescence, Western blotting, and both chromogenic and single-molecule in situ hybridizations, we validated AKI signatures in multiple experiments. RESULTS Our findings show the time course of changing gene expression patterns for multiple AKI stages and all renal cell types. We observed elevated expression of crucial injury response factors-including kidney injury molecule-1 (Kim1), lipocalin 2 (Lcn2), and keratin 8 (Krt8)-and of several novel genes (Ahnak, Sh3bgrl3, and Col18a1) not previously examined in kidney pathologies. AKI induced proximal tubule dedifferentiation, with a pronounced nephrogenic signature represented by Sox4 and Cd24a. Moreover, AKI caused the formation of "mixed-identity cells" (expressing markers of different renal cell types) that are normally seen only during early kidney development. The injured tubules acquired a proinflammatory and profibrotic phenotype; moreover, AKI dramatically modified ligand-receptor crosstalk, with potential pathologic epithelial-to-stromal interactions. Advancing age in AKI onset was associated with maladaptive response and kidney fibrosis. CONCLUSIONS The scRNA-seq, comprehensive, cell-specific profiles provide a valuable resource for examining molecular pathways that are perturbed in AKI. The results fully define AKI-associated dedifferentiation programs, potential pathologic ligand-receptor crosstalk, novel genes, and the improved injury response in younger mice, and highlight potential targets of kidney injury.
New Hepatic Resection Criteria for Intermediate-Stage Hepatocellular Carcinoma Can Improve Long-Term Survival: A Retrospective, Multicenter Collaborative Study

Background: Hepatic resection (HR) is not recommended for intermediate-stage hepatocellular carcinoma (HCC) by the Barcelona Clinic Liver Cancer criteria. We examined the prognostic factors of HR for intermediate-stage HCC and developed new HR criteria for intermediate-stage HCC. Methods: A total of 110 patients who underwent HR without any prior treatment for intermediate-stage HCC between January 2007 and December 2012 were enrolled at eight university hospitals. The outcomes and prognostic factors of HR were evaluated to develop new HR criteria. Results: In terms of tumor size and number, the most significant prognostic factors were within the up-to-seven criteria. Furthermore, serum albumin level ≥35 g/L and serum alpha-fetoprotein (AFP) level <100 µg/L were prognostic factors in multivariate analysis. The 5-year cumulative survival rate of patients based on the new HR criteria (i.e., up-to-seven, AFP <100 µg/L, albumin ≥35 g/L) was 81.4% and the area under the curve was 0.653. Conclusions: HR can improve the prognosis of patients with intermediate-stage HCC who meet the up-to-seven criteria and have serum albumin levels ≥35 g/L and serum AFP levels <100 µg/L. These factors could serve as new HR criteria for intermediate-stage HCC.
Refined Carbohydrate Consumption and Facial Attractiveness

Since the second half of the 20th century, a massive increase in the consumption of refined carbohydrates has occurred, generating well-described detrimental health effects such as obesity, insulin resistance, type II diabetes, cardiovascular diseases and dental caries. Certain physiological mechanisms involved, particularly through chronic hyperglycaemia and hyperinsulinaemia, suggest that a non-medical trait such as facial attractiveness could also be affected. To explore this possibility, variation in facial attractiveness was evaluated relative to refined carbohydrate consumption. Attractiveness was assessed from facial pictures as judged by raters of the opposite sex. Estimates of refined carbohydrate consumption were based on the glycaemic load of three mealtimes at-higher glycaemic risk (breakfast, afternoon snack and between-meal snack). In the presence of several control variables, facial pictures of women and men with higher between-meal glycaemic loads were preferred by opposite-sex raters. Structural equation modeling suggests that this result is possibly mediated by an increase in apparent age for men and an increase in femininity for women. The different physiological ecologies of the three meals at-higher glycaemic risk are discussed as well as the interpretation of the results in terms of adaptation or maladaptation to the modern and unique dietary environment.
Precise Editing of the OsPYL9 Gene by RNA-Guided Cas9 Nuclease Confers Enhanced Drought Tolerance and Grain Yield in Rice (Oryza sativa L.) by Regulating Circadian Rhythm and Abiotic Stress Responsive Proteins

Abscisic acid (ABA) is involved in regulating drought tolerance, and pyrabactin resistance-like (PYL) proteins are known as ABA receptors. To elucidate the role of one of the ABA receptors in rice, OsPYL9 was mutagenized through CRISPR/Cas9 in rice. Homozygous and heterozygous mutant plants lacking any off-targets and T-DNA were screened based on site-specific sequencing and used for morpho-physiological, molecular, and proteomic analysis. Mutant lines appear to accumulate higher ABA, antioxidant activities, chlorophyll content, leaf cuticular wax, and survival rate, whereas a lower malondialdehyde level, stomatal conductance, transpiration rate, and vascular bundles occur under stress conditions. Proteomic analysis found a total of 324 differentially expressed proteins (DEPs), out of which 184 and 140 were up and downregulated, respectively. The OsPYL9 mutants showed an increase in grain yield under both drought and well watered field conditions. Most of the DEPs related to circadian clock rhythm, drought response, and reactive oxygen species were upregulated in the mutant plants. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DEPs were only involved in circadian rhythm and Gene Ontology (GO) analysis showed that most of the DEPs were involved in response to abiotic stimulus, and abscisic acid-activated signaling pathways. Protein GIGANTEA, Adagio-like, and Pseudo-response regulator proteins showed higher interaction in protein–protein interaction (PPI) network. Thus, the overall results showed that CRISPR/Cas9-generated OsPYL9 mutants have potential to improve both drought tolerance and the yield of rice. Furthermore, global proteome analysis provides new potential biomarkers and understandings of the molecular mechanism of rice drought tolerance.
Group versus Individualised Minimum Velocity Thresholds in the Prediction of Maximal Strength in Trained Female Athletes

This study examined the accuracy of different velocity-based methods in the prediction of bench press and squat one-repetition maximum (1RM) in female athletes. Seventeen trained females (age 17.8 ± 1.3 years) performed an incremental loading test to 1RM on bench press and squat with the mean velocity being recorded. The 1RM was estimated from the load–velocity relationship using the multiple- (8 loads) and two-point (2 loads) methods and group and individual minimum velocity thresholds (MVT). No significant effect of method, MVT or interaction was observed for the two exercises (p > 0.05). For bench press and squat, all prediction methods demonstrated very large to nearly perfect correlations with respect to the actual 1RM (r range = 0.76 to 0.97). The absolute error (range = 2.1 to 3.8 kg) for bench press demonstrated low errors that were independent of the method and MVT used. For squat, the favorable group MVT errors for the multiple- and two-point methods (absolute error = 7.8 and 9.7 kg, respectively) were greater than the individual MVT errors (absolute error = 4.9 and 6.3 kg, respectively). The 1RM can be accurately predicted from the load–velocity relationship in trained females, with the two-point method offering a quick and less fatiguing alternative to the multiple-point method.
Contrastive Similarity Matching for Supervised Learning

Abstract We propose a novel biologically plausible solution to the credit assignment problem motivated by observations in the ventral visual pathway and trained deep neural networks. In both, representations of objects in the same category become progressively more similar, while objects belonging to different categories become less similar. We use this observation to motivate a layer-specific learning goal in a deep network: each layer aims to learn a representational similarity matrix that interpolates between previous and later layers. We formulate this idea using a contrastive similarity matching objective function and derive from it deep neural networks with feedforward, lateral, and feedback connections and neurons that exhibit biologically plausible Hebbian and anti-Hebbian plasticity. Contrastive similarity matching can be interpreted as an energy-based learning algorithm, but with significant differences from others in how a contrastive function is constructed.
Preclinical and Clinical Applications of Biomaterials in the Enhancement of Wound Healing in Oral Surgery: An Overview of the Available Reviews

Oral surgery has undergone dramatic developments in recent years due to the use of biomaterials. The aim of the present review is to provide a general overview of the current biomaterials used in oral surgery and to comprehensively outline their impact on post-operative wound healing. A search in Medline was performed, including hand searching. Combinations of searching terms and several criteria were applied for study identification, selection, and inclusion. The literature was searched for reviews published up to July 2020. Reviews evaluating the clinical and histological effects of biomaterials on post-operative wound healing in oral surgical procedures were included. Review selection was performed by two independent reviewers. Disagreements were resolved by a third reviewer, and 41 reviews were included in the final selection. The selected papers covered a wide range of biomaterials such as stem cells, bone grafts, and growth factors. Bioengineering and biomaterials development represent one of the most promising perspectives for the future of oral surgery. In particular, stem cells and growth factors are polarizing the focus of this ever-evolving field, continuously improving standard surgical techniques, and granting access to new approaches.