Miracle-dz/UniFAR-FTUs huggingface dataset:
Studies on variability, heritability and genetic advance in garlic (Allium sativum L)

Among the spices grown in India, garlic (Allium sativum L.) is undoubtebly one of the important crops of alliaceae after onion and propagated vegetatively. It is also used as flavor agent and in pharmaceutical preparation due to its high valid medicinal properties like antimicrobial, antidiabetic and anticarcinogenic action. Garlic has higher nutritive value than other bulb crops (Pandey, 1989) and has good export potential as fresh bulb as well as in the dehydrated form (Gupta and Singh, 1998). During 200910, the garlic was grown on an area of 107.69 thousand hectare and estimated production was approximately 593.10 thousands MT. The average productivity of garlic in India is 5.00 t/ha, which is quite low as compared to other garlic growing countries. To meet out the domestic requirement and to fulfill the export demand, selection of suitable variety for growing under different agroclimatic condition is necessary. As this crop is propagated vegetatively, the clonal selection is an important breeding method and very scanty work has been done on the association between different traits, which are prerequisites for executing a selection programme for complex quantitative yield. With a view to develop high yielding garlic varieties the National Horticultural Research and Development Foundation (NHRDF), Nashik collected a good numbers of germplasm across the country and abroad and conducted field experiment to assess the potential of genetic resources to identify cloves having high bulb yield with large sized cloves, less number of clove per bulb and other desirable traits.
Areas of white matter hyperintensities and motor symptoms of Parkinson disease

Objective To determine whether deep white matter and periventricular hyperintensities affect the motor symptoms of Parkinson disease (PD) differently, we analyzed MRI and dopamine transporter imaging. Methods We analyzed the medical records of patients with de novo PD who underwent dopamine transporter PET scanning and MRI at their first visit. Deep white matter and periventricular hyperintensities were scored with a visual rating scale, and motor symptoms were assessed by Unified Parkinson's Disease Rating Scale motor score and tremor, rigidity, bradykinesia, and axial symptom subscores. The influence of white matter hyperintensity on motor symptoms was explored using multivariable linear regression models. Results A total of 93 patients (mean age, 67.2 ± 9.9 years; 44 male) were included and the mean motor score was 25.0 ± 10.8. Subscores for bradykinesia and axial symptoms were correlated with both deep white matter and periventricular hyperintensities scores. Multivariable linear regression models revealed that deep white matter hyperintensities score was significantly associated with subscore for bradykinesia and periventricular hyperintensities score was associated with subscores for bradykinesia and axial symptoms after adjusting for putaminal dopamine transporter availability and clinical factors. Conclusions These results demonstrate that deep white matter hyperintensities are associated with bradykinesia and periventricular hyperintensities are associated with bradykinesia and axial symptoms in patients with PD independently of the severity of dopaminergic depletion.
The MD Anderson Prostate Cancer Patient-derived Xenograft Series (MDA PCa PDX) Captures the Molecular Landscape of Prostate Cancer and Facilitates Marker-driven Therapy Development

Purpose: Advances in prostate cancer lag behind other tumor types partly due to the paucity of models reflecting key milestones in prostate cancer progression. Therefore, we develop clinically relevant prostate cancer models. Experimental Design: Since 1996, we have generated clinically annotated patient-derived xenografts (PDXs; the MDA PCa PDX series) linked to specific phenotypes reflecting all aspects of clinical prostate cancer. Results: We studied two cell line–derived xenografts and the first 80 PDXs derived from 47 human prostate cancer donors. Of these, 47 PDXs derived from 22 donors are working models and can be expanded either as cell lines (MDA PCa 2a and 2b) or PDXs. The histopathologic, genomic, and molecular characteristics (androgen receptor, ERG, and PTEN loss) maintain fidelity with the human tumor and correlate with published findings. PDX growth response to mouse castration and targeted therapy illustrate their clinical utility. Comparative genomic hybridization and sequencing show significant differences in oncogenic pathways in pairs of PDXs derived from different areas of the same tumor. We also identified a recurrent focal deletion in an area that includes the speckle-type POZ protein-like (SPOPL) gene in PDXs derived from seven human donors of 28 studied (25%). SPOPL is a SPOP paralog, and SPOP mutations define a molecular subclass of prostate cancer. SPOPL deletions are found in 7% of The Cancer Genome Atlas prostate cancers, which suggests that our cohort is a reliable platform for targeted drug development. Conclusions: The MDA PCa PDX series is a dynamic resource that captures the molecular landscape of prostate cancers progressing under novel treatments and enables optimization of prostate cancer–specific, marker-driven therapy.
Synthesis of Atomically Thin Hexagonal Diamond with Compression.

Atomically thin diamond, also called diamane, is a two-dimensional carbon allotrope and has attracted considerable scientific interest because of its potential physical properties. However, the successful synthesis of a pristine diamane has up until now not been achieved. We demonstrate the realization of a pristine diamane through diamondization of mechanically exfoliated few-layer graphene via compression. Resistance, optical absorption, and x-ray diffraction measurements reveal that hexagonal diamane (h-diamane) with a bandgap of 2.8 ± 0.3 eV forms by compressing tri-layer and thicker graphene to above 20 GPa at room temperature and can be preserved upon decompression to ~1.0 GPa. Theoretical calculations indicate that a (-2110)-oriented h-diamane is energetically stable and has a lower enthalpy than its few-layer graphene precursor above the transition pressure. Compared to gapless graphene, semiconducting h-diamane offers exciting possibilities for carbon-based electronic devices.
Connecting Embeddings for Knowledge Graph Entity Typing

Knowledge graph (KG) entity typing aims at inferring possible missing entity type instances in KG, which is a very significant but still under-explored subtask of knowledge graph completion. In this paper, we propose a novel approach for KG entity typing which is trained by jointly utilizing local typing knowledge from existing entity type assertions and global triple knowledge in KGs. Specifically, we present two distinct knowledge-driven effective mechanisms of entity type inference. Accordingly, we build two novel embedding models to realize the mechanisms. Afterward, a joint model via connecting them is used to infer missing entity type instances, which favors inferences that agree with both entity type instances and triple knowledge in KGs. Experimental results on two real-world datasets (Freebase and YAGO) demonstrate the effectiveness of our proposed mechanisms and models for improving KG entity typing. The source code and data of this paper can be obtained from: https://github.com/Adam1679/ConnectE .
Estrus and ovulation responses in anestrus postpartum swamp buffaloes following synchronization with a controlled internal drug release device and prostaglandin F2α based protocols.

The objectives were to determine the estrus and ovulation responses to the controlled internal drug release (CIDR) and prostaglandin F2α (PGF2α) protocol and to compare the efficacy of this protocol with CIDR-PGF2α based protocols in combination with gonadotropin-releasing hormone (GnRH) or pregnant mare serum gonadotropin (PMSG); with or without human chorionic gonadotropin (hCG) administration in thirty-eight anestrus postpartum Swamp buffalo cows. In experiment 1 (control group): ten cows received CIDR inserts for 10 d and were treated with PGF2α immediately after CIDR withdrawal. In experiment 2, twenty-eight cows were divided into four equal groups; I: CIDR-PGF2α+GnRH, II: CIDRPGF2α+GnRH+hCG, III: CIDR-PGF2α+PMSG and IV: CIDR-PGF2α+PMSG+hCG. Each cow received an intravaginal CIDR for 10 d and PGF2α immediately after CIDR withdrawal. The GnRH or PMSG was administered immediately after CIDR removal. The hCG was administered 48 h after CIDR withdrawal. In experiment 1, 90% of cows showed estrus responses and 40.00% ovulation rate. In experiment 2, all cows showed estrus responses. The ovulation rates of Groups I, II, III and IV were not different. Moreover, the ovulation rates in Groups I and II were higher than the control group (P≤0.05). The CIDR-PGF2α synchronization was found to produce positive estrus and ovulation responses and all of the CIDRPGF2α based protocols were found to be equally effective in improving the ovulation rate in anestrus postpartum buffalo cows.
Staphylococcus aureus bacteremia at a referral medical center in Kenya: A retrospective review of cases from 2010 to 2018

Background Many studies have shown that Staphylococcus aureus is a leading cause of both community onset and hospital onset bloodstream infections. However, relatively little is known about the occurrence and outcome of S. aureus bacteremia in sub-Saharan Africa. A previous report indicated that S. aureus accounts for 16% of community onset and 6% of hospital onset bloodstream infections at Aga Khan University Hospital Nairobi (AKUHN). Data about the etiology of S. aureus bacteremia in sub-Saharan Africa will help optimize recognition and treatment. This study was performed in order to understand the etiologies and risk factors for S. aureus bacteremia in a sub-Saharan location. Materials and methods A review of the electronic record of laboratory results from September 2010 through December 2018 identified 201 patients seen at AKUHN with S. aureus bacteremia. The source and/or focus of infection was identified and in-hospital mortality was determined. Cases with bacteremia after three days of hospitalization were considered hospital acquired. Community onset cases were divided into community acquired and health care associated. Results Most cases (71%; 143/201) were community onset, but only 41% (83/201) of these cases were community acquired. The most commonly identified foci of infection for community acquired bacteremia were musculoskeletal (25%; 21/83) and skin and soft tissue (24%; 20/83). The majority of health care associated (70%; 40/57) and hospital acquired cases (74%; 43/58) were associated with invasive vascular devices, with peripheral IVs being the most common for hospital acquired and dialysis catheters being the most common for health care associated infections. In-hospital mortality rates were 23% (19/83) for community acquired, 19% (11/57) for health care associated and 33% (19/58) for hospital acquired infections. Conclusion Invasive vascular devices were associated with a substantial portion of cases of S. aureus bacteremia and provide an important target for infection control efforts.
SAS: Dialogue State Tracking via Slot Attention and Slot Information Sharing

Dialogue state tracker is responsible for inferring user intentions through dialogue history. Previous methods have difficulties in handling dialogues with long interaction context, due to the excessive information. We propose a Dialogue State Tracker with Slot Attention and Slot Information Sharing (SAS) to reduce redundant information’s interference and improve long dialogue context tracking. Specially, we first apply a Slot Attention to learn a set of slot-specific features from the original dialogue and then integrate them using a slot information sharing module. Our model yields a significantly improved performance compared to previous state-of the-art models on the MultiWOZ dataset.
Predictors of infection-related rehospitalization in heart failure patients and its impact on long-term survival

Supplemental Digital Content is available in the text Background Infection is the most common non-cardiovascular cause of re-hospitalizations for heart failure patients. We therefore investigated the predictors of infection-related re-hospitalization (IRRH) in heart failure patients and its impact on long-term survival. Methods and Results We prospectively recruited 622 patients after the index hospitalization for decompensated heart fail with primary endpoints of IRRH and all-cause mortality. During follow-up of 3.9 ± 2.7 years, IRRHs occurred in 104 (16.7%) patients. Of the 104 patients who experienced IRRHs, the time from the index hospitalization to IRRH was 1.0 (interquartile range: 0.4–2.6) years. Independent predictors of IRRH were age (hazard ratio: 1.02, 95% confidence interval: 1.01–1.04), diabetes mellitus (2.12, 1.42–3.17), not taking angiotensin-converting enzyme inhibitors or angiotensin II receptor blockers (1.67, 1.01–2.78), needing maintenance therapy with a loop diuretic (2.10, 1.36–3.26), hemoglobin levels (0.87, 0.79–0.96), and estimated glomerular filtration rates (eGFRs) (0.99, 0.98–0.99). IRRH independently predicted all-cause mortality (1.99, 1.32–2.98) after adjusting for age, body mass index, New York Heart Association functional class, chronic obstructive pulmonary disease, brain natriuretic peptide, hemoglobin, and eGFR. The increased risk of death associated with IRRHs was predominantly for lower respiratory tract infections (3.71, 2.28–6.04), urogenital tract infections (2.83, 1.32–6.10), and sepsis (3.26, 1.20–8.85). Conclusion IRRHs in patients discharged for acute decompensated heart fail independently predicted worse long-term survival. We further identified independent predictors of IRRHs. These findings warrant future studies for tackling IRRH.
Stock Embeddings Acquired from News Articles and Price History, and an Application to Portfolio Optimization

Previous works that integrated news articles to better process stock prices used a variety of neural networks to predict price movements. The textual and price information were both encoded in the neural network, and it is therefore difficult to apply this approach in situations other than the original framework of the notoriously hard problem of price prediction. In contrast, this paper presents a method to encode the influence of news articles through a vector representation of stocks called a stock embedding. The stock embedding is acquired with a deep learning framework using both news articles and price history. Because the embedding takes the operational form of a vector, it is applicable to other financial problems besides price prediction. As one example application, we show the results of portfolio optimization using Reuters & Bloomberg headlines, producing a capital gain 2.8 times larger than that obtained with a baseline method using only stock price data. This suggests that the proposed stock embedding can leverage textual financial semantics to solve financial prediction problems.
Interpreting Pretrained Contextualized Representations via Reductions to Static Embeddings

Contextualized representations (e.g. ELMo, BERT) have become the default pretrained representations for downstream NLP applications. In some settings, this transition has rendered their static embedding predecessors (e.g. Word2Vec, GloVe) obsolete. As a side-effect, we observe that older interpretability methods for static embeddings — while more diverse and mature than those available for their dynamic counterparts — are underutilized in studying newer contextualized representations. Consequently, we introduce simple and fully general methods for converting from contextualized representations to static lookup-table embeddings which we apply to 5 popular pretrained models and 9 sets of pretrained weights. Our analysis of the resulting static embeddings notably reveals that pooling over many contexts significantly improves representational quality under intrinsic evaluation. Complementary to analyzing representational quality, we consider social biases encoded in pretrained representations with respect to gender, race/ethnicity, and religion and find that bias is encoded disparately across pretrained models and internal layers even for models with the same training data. Concerningly, we find dramatic inconsistencies between social bias estimators for word embeddings.
Influence of Sociodemographic, Premorbid, and Injury-Related Factors on Post-Concussion Symptoms after Traumatic Brain Injury

Background: Post-concussion symptoms (PCS) are often reported as consequences of mild and moderate traumatic brain injury (TBI), but these symptoms are not well documented in severe TBI. There is a lack of agreement as to which factors and covariates affect the occurrence, frequency, and intensity of PCS among TBI severity groups. The present study therefore aims to examine the association between sociodemographic, premorbid, and injury-related factors and PCS. Methods: A total of 1391 individuals (65% male) from the CENTER-TBI study were included in the analyses. The occurrence, frequency (number of PCS), and intensity (severity) of PCS were assessed using the Rivermead Post-concussion Symptoms Questionnaire (RPQ) at six months after TBI. To examine the association between selected factors (age, sex, living situation, employment status, educational background, injury and TBI severity, and premorbid problems) and PCS, a zero-inflated negative binomial model (ZINB) for occurrence and frequency of PCS and a standard negative binomial regression (NB) for intensity were applied. Results: Of the total sample, 72% of individuals after TBI reported suffering from some form of PCS, with fatigue being the most frequent among all TBI severity groups, followed by forgetfulness, and poor concentration. Different factors contributed to the probability of occurrence, frequency, and intensity of PCS. While the occurrence of PCS seemed to be independent of the age and sex of the individuals, both the frequency and intensity of PCS are associated with them. Both injury and TBI severity influence the occurrence and frequency of PCS, but are associated less with its intensity (except “acute” symptoms such as nausea, vomiting, and headaches). Analyses focusing on the mTBI subgroup only yielded results comparable to those of the total sample. Discussion: In line with previous studies, the results support a multifactorial etiology of PCS and show the importance of differentiating between their occurrence, frequency, and intensity to better provide appropriate treatment for individual subgroups with different symptoms (e.g., multiple PCS or more intense PCS). Although PCS often occur in mild to moderate TBI, individuals after severe TBI also suffer from PCS or post-concussion-like symptoms that require appropriate treatment. The chosen statistical approaches (i.e., ZINB and NB models) permit an ameliorated differentiation between outcomes (occurrence, frequency, and intensity of PCS) and should be used more widely in TBI research.
Complementary Feeding in Preterm Infants: A Systematic Review

Background: This systematic review summarizes available literature regarding complementary feeding (CF) in preterm infants, with or without comorbidities that may interfere with oral functions. Methods: A literature search was conducted in PubMed and the Cochrane Library. Studies relating to preterm infants (gestational age <37 weeks) were included in the analysis. Retrieved papers were categorized according to their main topic: CF timing and quality; clinical outcome; recommendations; strategies in infants with oral dysfunction. Results: The literature search in PubMed retrieved 6295 papers. Forty met inclusion criteria. The Cochrane search identified four additional study protocols, two related to studies included among PubMed search results, and two ongoing trials. Moreover, among 112 papers dealing with oral feeding, four aiming at managing CF in preterm infants with oral dysfunctions were identified. Conclusions: The available literature does not provide specific guidelines on the management of CF in preterm infants, who are generally weaned earlier than term infants. There is a paucity of data regarding the relationship between CF and growth/quality of growth and health outcomes in preterm infants. It could be suggested to start CF between five and eight months of chronological age if infants have reached three months corrected age and if they have acquired the necessary developmental skills. An individualized multidisciplinary intervention is advisable for preterm infants with oral dysfunctions.
A pre‐existing coordinated inflammatory microenvironment is associated with complete response of vulvar high‐grade squamous intraepithelial lesions to different forms of immunotherapy

Immunotherapy of vulvar high‐grade squamous intraepithelial lesion (vHSIL) is investigated as an alternative for surgery, because of high comorbidity and risk of recurrence. Limited evidence exists on the role and composition of the immune microenvironment in current immunotherapeutic approaches for vHSIL. The vHSIL of 29 patients biopsied before treatment with imiquimod were analyzed by two multiplex seven‐color immunofluorescence panels to investigate the pre‐existing T‐cell and myeloid cell composition in relation to treatment response. The samples were scanned with the Vectra multispectral imaging system. Cells were automatically phenotyped and counted with inForm advanced image analysis software. Cell counts and composition were compared to that of vHSIL patients before therapeutic vaccination (n = 29) and to healthy vulva (n = 27). Our data show that the immune microenvironment of complete responders (CR) to imiquimod resembled the coordinated infiltration with type 1 CD4+ and CD8+ T cells and CD14+ inflammatory myeloid cells also found in healthy vulva. However, more CD8+ T cells and FoxP3+ regulatory T cells were present in CR. The lesions of partial responders (PR) lacked such a coordinated response and displayed an impaired influx of CD14+ inflammatory myeloid cells. Importantly, complete responses after imiquimod or therapeutic vaccination showed the same dependency on a pre‐existing coordinated type 1 T‐cell and CD14+ myeloid cell infiltration. In conclusion, a good clinical outcome after two different forms of immunotherapy for vHSIL is associated with the presence of a primary inflammatory process resulting in the coordinated influx of several types of immune cells which is then amplified.