Takshan/R1 huggingface dataset:
Langerian mindfulness, quality of life and psychological symptoms in a sample of Italian students.

BACKGROUND: Noticing new things, accepting the continuously changing nature of circumstances, and flexibly shifting perspectives in concert with changing contexts constitute the essential features of Langerian mindfulness. This contrasts with a "mindless" approach in which one remains fixed in a singular mindset and is closed off to new possibilities. Despite potentially important clinical applications for this construct, few studies have explored them. The instrument developed to measure Langerian mindfulness is the Langer Mindfulness Scale (LMS), although this tool has been limited primarily to English-speaking populations. The study aimed to test LMS validity in the Italian language and to analyze the relationships between Langerian mindfulness and well-being. METHODS: We translated the LMS into Italian, analyzed its factor structure, and investigated the correlation between mindfulness and quality of life and psychological well-being in a sample of 248 Italian students (88.7% females, mean age 20.05). A confirmatory factor analysis confirmed the tri-dimensional structure of the English LMS in the Italian version. RESULTS: The primary analysis found a significant negative correlation between mindfulness and psychological symptoms including obsessive-compulsive tendencies, depression, anxiety, and paranoid ideation. There was also a positive correlation between mindfulness and reports of quality of life. CONCLUSIONS: The Italian LMS appears reliable and it shows relevant correlations with well-being.
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks.

Motivation: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction. Results: The new method, named SPOT-Disorder, has steadily improved over a similar method using a traditional, window-based neural network (SPINE-D) in all datasets tested without separate training on short and long disordered regions. Independent tests on four other datasets including the datasets from critical assessment of structure prediction (CASP) techniques and >10 000 annotated proteins from MobiDB, confirmed SPOT-Disorder as one of the best methods in disorder prediction. Moreover, initial studies indicate that the method is more accurate in predicting functional sites in disordered regions. These results highlight the usefulness combining LSTM with deep bidirectional recurrent neural networks in capturing non-local, long-range interactions for bioinformatics applications. Availability and Implementation: SPOT-disorder is available as a web server and as a standalone program at: http://sparks-lab.org/server/SPOT-disorder/index.php . Contact: j.hanson@griffith.edu.au or yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au. Supplementary information: Supplementary data is available at Bioinformatics online.
Discovery of new leads against Mycobacterium tuberculosis using scaffold hopping and shape based similarity.

BM212 [1,5-diaryl-2-methyl-3-(4-methylpiperazin-1-yl)-methyl-pyrrole] is a pyrrole derivative with strong inhibitory activity against drug resistant Mycobacterium tuberculosis and mycobacteria residing in macrophages. However, it was not pursued because of its poor pharmacokinetics and toxicity profile. Our goal was to design and synthesize new antimycobacterial BM212 analogs with lower toxicity and better pharmacokinetic profile. Using the scaffold hopping approach, three structurally diverse heterocycles - 2,3-disubstituted imidazopyridines, 2,3-disubstituted benzimidazoles and 1,2,4-trisubstituted imidazoles emerged as promising antitubercular agents. All compounds were synthesized through easy and convenient methods and their structures confirmed by IR, (1)H NMR, (13)C NMR and MS. In-vitro cytotoxicity studies on normal kidney monkey cell lines and HepG2 cell lines, as well as metabolic stability studies on rat liver microsomes for some of the most active compounds, established that these compounds have negligible cytotoxicity and are metabolically stable. Interestingly the benzimidazole compound (4a) is as potent as the parent molecule BM212 (MIC 2.3μg/ml vs 0.7-1.5μg/ml), but is devoid of the toxicity against HepG2 cell lines (IC50 203.10µM vs 7.8µM).
Differential expression of the HvCslF6 gene late in grain development may explain quantitative differences in (1,3;1,4)-β-glucan concentration in barley.

The cellulose synthase-like gene HvCslF6, which is essential for (1,3;1,4)-β-glucan biosynthesis in barley, collocates with quantitative trait loci (QTL) for grain (1,3;1,4)-β-glucan concentration in several populations, including CDC Bold × TR251. Here, an alanine-to-threonine substitution (caused by the only non-synonymous difference between the CDC Bold and TR251 HvCslF6 alleles) was mapped to a position within HvCSLF6 that seems unlikely to affect enzyme stability or function. Consistent with this, transient expression of full-length HvCslF6 cDNAs from CDC Bold and TR251 in Nicotiana benthamiana led to accumulation of similar amounts of (1,3;1,4)-β-glucan accumulation. Monitoring of HvCslF6 transcripts throughout grain development revealed a significant difference late in grain development (more than 30 days after pollination), with TR251 [the parent with higher grain (1,3;1,4)-β-glucan] exhibiting higher transcript levels than CDC Bold. A similar difference was observed between Beka and Logan, the parents of another population in which a QTL had been mapped in the HvCslF6 region. Sequencing of a putative promoter region of HvCslF6 revealed numerous polymorphisms between CDC Bold and TR251, but none between Beka and Logan. While the results of this work indicate that naturally occurring quantitative differences in (1,3;1,4)-β-glucan accumulation may be due to cis-regulated differences in HvCslF6 expression, these could not be attributed to any specific DNA sequence polymorphism. Nevertheless, information on HvCslF6 sequence polymorphism was used to develop molecular markers that could be used in barley breeding to select for the desired [low or high (1,3;1,4)-β-glucan] allele of the QTL.
Bedside analysis of the sublingual microvascular glycocalyx in the emergency room and intensive care unit - the GlycoNurse study.

BACKGROUND: Deterioration of the endothelial glycocalyx (eGC), a protective carbohydrate-rich layer lining the luminal surface of the endothelium, plays a key role in vascular barrier dysfunction and eventually organ-failure in systemic inflammatory response syndrome and sepsis. Early detection of glycocalyx damage could thus become an important goal in critical care. This study was designed to determine the feasibility and reproducibility of quantitative, real-time glycocalyx measurements performed at bedside in the emergency room (ER) and intensive care unit (ICU). METHODS: The observational study included 70 patients admitted to the ER or ICU of a university hospital. A physician and the nurse in charge of the patient performed sublingual microcirculatory measurements using sidestream dark field (SDF) imaging. A novel data acquisition and analysis software (GlycoCheck™) was used to analyze the perfused boundary region (PBR), an inverse parameter of endothelial glycocalyx dimensions in vessels with diameters of between 5 and 25 μm. RESULTS: The method showed a good intra-observer reproducibility. Specifically, intraclass correlation coefficient analysis showed an excellent reproducibility between the physician's measurements (0.77 [CI 95%: 0.52-0.89]). The bias between the two PBRs was - 0.077 ± 0.24 μm. Moreover, there were no significant differences in the PBR values obtained by the nurses when compared to those reported by the physician (regarded as the "gold standard" measurement). Intraclass correlation coefficient analysis showed excellent reproducibility between the nurses' and physician's PBRs (0.75 [95% CI: 0.52-0.87]). The mean difference between the two PBRs (i.e., the bias) was 0.007 ± 0.25 μm. The nurses' PBR assessment had a 90% sensitivity (95% CI: 60-99%) and 90% specificity (95% CI: 80-93%) to identify a severely impaired glycocalyx. CONCLUSION: Glycocalyx dimensions can be measured at patients' bedside precisely by non-invasive assessment of the PBR. This assessment could become part of standard monitoring and contribute to clinical decision-making and resuscitation protocols in clinical trials and daily practice.
Diversity in root growth responses to moisture deficit in young faba bean (Vicia faba L.) plants.

Background: Soil moisture deficiency causes yield reduction and instability in faba bean (Vicia faba L.) production. The extent of sensitivity to drought stress varies across accessions originating from diverse moisture regimes of the world. Hence, we conducted successive greenhouse experiments in pots and rhizotrons to explore diversity in root responses to soil water deficit. Methods: A set of 89 accessions from wet and dry growing regions of the world was defined according to the Focused Identification of Germplasm Strategy and screened in a perlite-sand medium under well watered conditions in a greenhouse experiment. Stomatal conductance, canopy temperature, chlorophyll concentration, and root and shoot dry weights were recorded during the fifth week of growth. Eight accessions representing the range of responses were selected for further investigation. Starting five days after germination, they were subjected to a root phenotyping experiment using the automated phenotyping platform GROWSCREEN-Rhizo. The rhizotrons were filled with peat-soil under well watered and water limited conditions. Root architectural traits were recorded five, 12, and 19 days after the treatment (DAT) began. Results: In the germplasm survey, accessions from dry regions showed significantly higher values of chlorophyll concentration, shoot and root dry weights than those from wet regions. Root and shoot dry weight as well as seed weight, and chlorophyll concentration were positively correlated with each other. Accession DS70622 combined higher values of root and shoot dry weight than the rest. The experiment in GROWSCREEN-Rhizo showed large differences in root response to water deficit. The accession by treatment interactions in taproot and second order lateral root lengths were significant at 12 and 19 DAT, and the taproot length was reduced up to 57% by drought. The longest and deepest root systems under both treatment conditions were recorded by DS70622 and DS11320, and total root length of DS70622 was three times longer than that of WS99501, the shortest rooted accession. The maximum horizontal distribution of a root system and root surface coverage were positively correlated with taproot and total root lengths and root system depth. DS70622 and WS99501 combined maximum and minimum values of these traits, respectively. Thus, roots of DS70622 and DS11320, from dry regions, showed drought-avoidance characteristics whereas those of WS99501 and Mèlodie/2, from wet regions, showed the opposite. Discussion: The combination of the germplasm survey and use of GROWSCREEN-Rhizo allowed exploring of adaptive traits and detection of root phenotypic markers for potential drought avoidance. The greater root system depth and root surface coverage, exemplified by DS70622 and DS11320, can now be tested as new sources of drought tolerance.
Inverse treatment planning for spinal robotic radiosurgery: an international multi-institutional benchmark trial.

Stereotactic radiosurgery (SRS) is the accurate, conformal delivery of high-dose radiation to well-defined targets while minimizing normal structure doses via steep dose gradients. While inverse treatment planning (ITP) with computerized optimization algorithms are routine, many aspects of the planning process remain user-dependent. We performed an international, multi-institutional benchmark trial to study planning variability and to analyze preferable ITP practice for spinal robotic radiosurgery. 10 SRS treatment plans were generated for a complex-shaped spinal metastasis with 21 Gy in 3 fractions and tight constraints for spinal cord (V14Gy &lt; 2 cc, V18Gy &lt; 0.1 cc) and target (coverage &gt; 95%). The resulting plans were rated on a scale from 1 to 4 (excellent-poor) in five categories (constraint compliance, optimization goals, low-dose regions, ITP complexity, and clinical acceptability) by a blinded review panel. Additionally, the plans were mathemati-cally rated based on plan indices (critical structure and target doses, conformity, monitor units, normal tissue complication probability, and treatment time) and compared to the human rankings. The treatment plans and the reviewers' rankings varied substantially among the participating centers. The average mean overall rank was 2.4 (1.2-4.0) and 8/10 plans were rated excellent in at least one category by at least one reviewer. The mathematical rankings agreed with the mean overall human rankings in 9/10 cases pointing toward the possibility for sole mathematical plan quality comparison. The final rankings revealed that a plan with a well-balanced trade-off among all planning objectives was preferred for treatment by most par-ticipants, reviewers, and the mathematical ranking system. Furthermore, this plan was generated with simple planning techniques. Our multi-institutional planning study found wide variability in ITP approaches for spinal robotic radiosurgery. The participants', reviewers', and mathematical match on preferable treatment plans and ITP techniques indicate that agreement on treatment planning and plan quality can be reached for spinal robotic radiosurgery.
Effects of Continuing Oral Risperidone vs. Switching from Risperidone to Risperidone Long-Acting Injection on Cognitive Function in Stable Schizophrenia Patients: A Pilot Study.

Objectives: Risperidone is the first new generation antipsychotic drug to become available as a long-acting injection (LAI). The purpose of this study was to evaluate the effects of switching from oral risperidone to risperidone LAI (RLAI) on cognitive function in stable schizophrenia patients compared with the effects of continuing oral risperidone. Methods: Sixteen stable patients who had received risperidone monotherapy for at least 3 months were enrolled (the RLAI group). Before and 24 weeks after switching to RLAI, the Japanese-language version of the Brief Assessment of Cognition in Schizophrenia (BACS-J) and the Positive and Negative Syndrome Scale (PANSS) were administered. To exclude the possibility of learning effects on the BACS-J results, 14 patients with stable schizophrenia who continued oral risperidone treatment were also assessed (the RIS group). Results: The two groups did not differ with respect to changes in the PANSS score, and no emergent side effects, including extrapyramidal symptoms, were observed. The BACS-J score for verbal memory exhibited greater improvement in the RLAI group than in the RIS group (p = 0.047). Conclusion: The results of this preliminary study suggest that switching from oral risperidone to RLAI may improve verbal capability more than continuing with oral risperidone. However, these findings must be replicated in a larger, double-blind study.
A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data.

Motivation: Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared with the huge amount of features (p). This 'n≪p' property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating external gene network information could be a potential solution to this issue. Still, the problem is very challenging because (i) there are tens of thousands of features and only hundreds of training samples, (ii) the scale-free structure of the gene network is unfriendly to the setup of convolutional neural networks. Results: To address these issues and build a robust classification model, we propose the Graph-Embedded Deep Feedforward Networks (GEDFN), to integrate external relational information of features into the deep neural network architecture. The method is able to achieve sparse connection between network layers to prevent overfitting. To validate the method's capability, we conducted both simulation experiments and real data analysis using a breast invasive carcinoma RNA-seq dataset and a kidney renal clear cell carcinoma RNA-seq dataset from The Cancer Genome Atlas. The resulting high classification accuracy and easily interpretable feature selection results suggest the method is a useful addition to the current graph-guided classification models and feature selection procedures. Availability and implementation: The method is available at https://github.com/yunchuankong/GEDFN. Supplementary information: Supplementary data are available at Bioinformatics online.
Upper extremity movement reliability and validity of the Kinect version 2.

PURPOSE: Studies have shown that marker-less motion detection systems, such as the first generation Kinect (Kinect 1), have good reliability and potential for clinical application. Studies of the second generation Kinect (Kinect 2) have shown a large range of accuracy relative to balance and joint localization; however, few studies have investigated the validity and reliability of the Kinect 2 for upper extremity motion. This investigation compared reliability and validity among the Kinect 1, Kinect 2 and a video motion capture (VMC) system for upper extremity movements. DESIGN: One healthy, adult male performed six upper extremity movements during two separate sessions. All movements were recorded on the Kinect 1, Kinect 2 and VMC simultaneously. Data were analyzed using MATLAB (Natick, MA), Microsoft Excel (Redmond, WA), and SPSS (Armonk, NY). RESULTS: Results indicated good reliability for both Kinects within a day; results between days were inconclusive for both devices due to the inability to exactly repeat the desired movements. Range of motion (ROM) magnitudes for both Kinects were different from the VMC, yet patterns of motion were very highly correlated for both devices. CONCLUSION: Simple transformations of Kinect data could bring magnitudes in line with those of the VMC, allowing the Kinects to be used in a clinical setting. Implications for Rehabilitation The clinical implications of the investigation support the notion that the Kinects could be used in the clinical setting if an understanding of their limitations exists. Using the Kinects to make assessments with a given data collection session is acceptable. Using the Kinects to make comparisons across different days such as before or after an intervention should be approached with caution. The Kinect 2 provides a more cost effective option compared to the VMC. Additionally, the Kinect is more portable, requires less time to set-up, and takes up less space, thus increasing its overall usability compared to the VMC.
Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore.

BACKGROUND: Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding. RESULTS: Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides. CONCLUSIONS: This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota.
Clinicopathologic and prognostic features of breast cancer in young women: a series from North of Morocco.

BACKGROUND: Literature data reported a higher frequency of breast cancer in young women (BCYW) in developing countries. BCYW is associated with delayed diagnosis, aggressive biology and poor prognosis. However, our knowledge of biological profile, treatment received and outcome of young patients is still limited in Morocco. We propose to analyze clinicopathologic, therapeutic and prognostic features of BCYW among a series of patients native and/or inhabitant of North of Morocco. METHODS: We carried out a retro-prospective study of 331 infiltrating breast cancer cases registered between January 2010 and December 2015. Details of tumor pathology, treatment and outcome were collected. Disease-Free Survival (DFS) and Overall Survival (OS) were assessed by Kaplan-Meier analysis. RESULTS: A total of 82 patients were diagnosed with breast cancer at the age of 40 or younger (24.8%). Median age was 36 years. More than one quarter (26%) of patients had family history of breast or ovarian cancer. Advanced stages accounted for 34.2% of cases. Median tumor diameter was 2.8 cm. Intermediate and high-grade tumors represented 47.6% and 40.2%, respectively. Nodal involvement was present in 58.5% and lymphovascular invasion was found in 47.7% of the patients. About two thirds (66.2%) of tumors were hormone receptor positive, 29.2% over-expressed HER2 receptor and 23% were triple negative. Patients underwent breast conserving surgery in 38.2% of cases, 61.7% were offered adjuvant chemotherapy and 84.6% received hormone therapy. Five-year DFS and OS were respectively 88.9% and 75.6%. Locoregional recurrence occurred in 2.8% of cases and 8.3% of patients developed distant metastases. CONCLUSION: Our findings are in accordance with previous studies that have shown a higher frequency of breast cancer among Moroccan young women. In line with literature data, clinicopathologic profile seems to be aggressive and prognosis is pejorative in our series.