Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodiversity patterns in interstitial marine microturbellaria: a case study within the genus Parotoplana (Platyhelminthes: Rhabditophora) with the description of four new species

Four new species of Otoplanidae (Platyhelminthes: Rhabditophora: Proseriata) with ranges restricted to the central Mediterranean are described. These species are characterized by the presence of a tubular copulatory stylet and by a bursa lacking an open connection to the atrium. Both characters are novel for the family Otoplanidae. The four species differ mainly in details of the morphology of the sclerotized structures of the copulatory organ. Generic attribution of the new species has been problematic. Morphological characters shared with either Parotoplanina or Parotoplanella were detected. Molecular data (based on 18S rRNA and 28S D1-D6 rRNA genes) evidenced that the new species constitute a monophyletic group falling within species of Parotoplana , with a sister/taxon relationship with Parotoplana spathifera. The genus Parotoplana , however, appears to be paraphyletic, as Parotoplanella progermaria nests within Parotoplana species. The inadequate molecular sampling, combined with the lack of sequences from the type species of both Parotoplana and Parotoplanina , suggested a cautionary taxonomic approach, and the new species are therefore attributed to the earliest generic taxon available, Parotoplana .
Targeted disruption of the glucocorticoid receptor gene blocks adrenergic chromaffin cell development and severely retards lung maturation.

The role of the glucocorticoid receptor (GR) in glucocorticoid physiology and during development was investigated by generation of GR-deficient mice by gene targeting. GR -/- mice die within a few hours after birth because of respiratory failure. The lungs at birth are severely atelectatic, and development is impaired from day 15.5 p.c. Newborn livers have a reduced capacity to activate genes for key gluconeogenic enzymes. Feedback regulation via the hypothalamic-pituitary-adrenal axis is severely impaired resulting in elevated levels of plasma adrenocorticotrophic hormone (15-fold) and plasma corticosterone (2.5-fold). Accordingly, adrenal glands are enlarged because of hypertrophy of the cortex, resulting in increased expression of key cortical steroid biosynthetic enzymes, such as side-chain cleavage enzyme, steroid 11 beta-hydroxylase, and aldosterone synthase. Adrenal glands lack a central medulla and synthesize no adrenaline. They contain no adrenergic chromaffin cells and only scattered noradrenergic chromaffin cells even when analyzed from the earliest stages of medulla development. These results suggest that the adrenal medulla may be formed from two different cell populations: adrenergic-specific cells that require glucocorticoids for proliferation and/or survival, and a smaller noradrenergic population that differentiates normally in the absence of glucocorticoid signaling.
Efficacy and Safety of Oncolytic Viruses in Randomized Controlled Trials: A Systematic Review and Meta-Analysis

Oncolytic virotherapy is a promising antitumor therapeutic strategy. It is based on the ability of viruses to selectively kill cancer cells and induce host antitumor immune responses. However, the clinical outcomes of oncolytic viruses (OVs) vary widely. Therefore, we performed a meta-analysis to illustrate the efficacy and safety of oncolytic viruses. The Cochrane Library, PubMed, and EMBASE databases were searched for randomized controlled trials (RCTs) published up to 31 January 2020. The data for objective response rate (ORR), overall survival (OS), progression-free survival (PFS), and adverse events (AEs) were independently extracted by two investigators from 11 studies that met the inclusion criteria. In subgroup analyses, the objective response rate benefit was observed in patients treated with oncolytic DNA viruses (odds ratio (OR) = 4.05; 95% confidence interval (CI): 1.96–8.33; p = 0.0002), but not in those treated with oncolytic RNA viruses (OR = 1.00, 95% CI: 0.66–1.52, p = 0.99). Moreover, the intratumoral injection arm yielded a statistically significant improvement (OR = 4.05, 95% CI: 1.96–8.33, p = 0.0002), but no such improvement was observed for the intravenous injection arm (OR = 1.00, 95% CI: 0.66–1.52, p = 0.99). Among the five OVs investigated in RCTs, only talimogene laherparepvec (T-VEC) effectively prolonged the OS of patients (hazard ratio (HR), 0.79; 95% CI: 0.63–0.99; p = 0.04). None of the oncolytic virotherapies improved the PFS (HR = 1.00, 95% CI: 0.85–1.19, p = 0.96). Notably, the pooled rate of severe AEs (grade ≥3) was higher for the oncolytic virotherapy group (39%) compared with the control group (27%) (risk difference (RD), 12%; risk ratio (RR), 1.44; 95% CI: 1.17–1.78; p = 0.0006). This review offers a reference for fundamental research and clinical treatment of oncolytic viruses. Further randomized controlled trials are needed to verify these results.
Completeness of intervention reporting in neurology randomized controlled trials: a retrospective, cross-sectional study.

AIM Incomplete reporting of interventions in randomized controlled trials (RCTs) may hinder the replicability of studies and thus lead to adverse clinical outcomes for patients. Currently, little is known about the completeness of intervention reporting in neurology clinical trials. This study's primary objective was to determine the completeness of intervention reporting in neurology RCTs, as measured by the Template for Intervention Description and Replication (TIDieR) checklist. The secondary objectives of this study were to compare the completeness of intervention reporting before and after TIDieR publication and to evaluate factors associated with intervention reporting. METHODS We conducted a cross-sectional, pilot-tested, double-blind investigation of 141 neurology RCTs to determine the completeness of intervention reporting in neurology. RESULTS Overall, the average number of TIDieR checklist items that reached completion per study was 7.4 out of 12 (61.7%). We found no increase in intervention reporting following the publication of TIDieR (P = 0.35). Our generalized estimating equation analysis found that poorer TIDieR adherence was associated with trials lacking a trial registration (P = 0.03). CONCLUSION Our findings showed that on average, authors reported only 61.7% of items on the TIDieR checklist. These findings have significant implications, because incomplete reporting may hinder the replicability of studies and thus negatively affect clinical outcomes for patients.
The majority of the matrix protein TapA is dispensable for Bacillus subtilis colony biofilm architecture

Biofilm formation is a co‐operative behaviour, where microbial cells become embedded in an extracellular matrix. This biomolecular matrix helps manifest the beneficial or detrimental outcome mediated by the collective of cells. Bacillus subtilis is an important bacterium for understanding the principles of biofilm formation. The protein components of the B. subtilis matrix include the secreted proteins BslA, which forms a hydrophobic coat over the biofilm, and TasA, which forms protease‐resistant fibres needed for structuring. TapA is a secreted protein also needed for biofilm formation and helps in vivo TasA‐fibre formation but is dispensable for in vitro TasA‐fibre assembly. We show that TapA is subjected to proteolytic cleavage in the colony biofilm and that only the first 57 amino acids of the 253‐amino acid protein are required for colony biofilm architecture. Through the construction of a strain which lacks all eight extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA function. It remains unknown why TapA is synthesised at 253 amino acids when the first 57 are sufficient for colony biofilm structuring; the findings do not exclude the core conserved region of TapA having a second role beyond structuring the B. subtilis colony biofilm.
Soybean seed quality reductions by high day and night temperature

Soybean Seed Quality Reductions by High Day and Night Temperature Environmental stress during reproductive growth of soybean [Glycine max (L.) Merr. ] may reduce seed germination and vigor. Most studies of environmental influence on soybean seed germination and vigor have concentrated on the effects of drought, maximum day temperature, or average daily temperature during seed fill. This study was conducted to determine the effects of different combinations of day temperatures and night temperatures during reproductive growth on soybean seed quality. Day/night temperatures of 30/20, 30/30, 35/ 20, and 35/30°C were imposed at flowering and pod set (R1-R5), seed fill and maturation (R5-R8), and during the entire reproductive growth period (R1-R8). High day and night temperature reduced soybean seed germination and seedling vigor. The extent of reductions in germination and vigor by high temperature was influenced by duration of temperature exposure and phase of reproductive growth. Temperatures during flowering and pod set exerted little influence on soybean seed quality. A combination of 35°C day temperature and 30°C night temperature during seed fill and maturation or 35°C day temperature from flowering to maturity decreased germination. Seedling vigor was reduced by 35/20, 30/30, and 35/30°C during seed fill and maturation and the entire reproductive period. Increase in night temperature from 20 to 30°C decreased seedling vigor at both 30 and 35°C day temperatures. These results suggest that locational and seasonal differences in soybean seed quality may be induced by high temperatures during reproductive growth and indicate that night temperatures along with day temperatures are important in determining soybean seed quality.
Unbiased yeast screens identify cellular pathways affected in Niemann–Pick disease type C

Three independent yeast genetic screens were performed identifying proteins and pathways contributing to the pathogenesis of NPC disease and suggesting new therapeutic avenues. Niemann–Pick disease type C (NPC) is a rare lysosomal storage disease caused by mutations in either the NPC1 or NPC2 genes. Mutations in the NPC1 gene lead to the majority of clinical cases (95%); however, the function of NPC1 remains unknown. To gain further insights into the biology of NPC1, we took advantage of the homology between the human NPC1 protein and its yeast orthologue, Niemann–Pick C–related protein 1 (Ncr1). We recreated the NCR1 mutant in yeast and performed screens to identify compensatory or redundant pathways that may be involved in NPC pathology, as well as proteins that were mislocalized in NCR1-deficient yeast. We also identified binding partners of the yeast Ncr1 orthologue. These screens identified several processes and pathways that may contribute to NPC pathogenesis. These included alterations in mitochondrial function, cytoskeleton organization, metal ion homeostasis, lipid trafficking, calcium signalling, and nutrient sensing. The mitochondrial and cytoskeletal abnormalities were validated in patient cells carrying mutations in NPC1, confirming their dysfunction in NPC disease.
Food Perishability and Inventory Management: A Comparison of Three Caching Strategies

Food stored for an extended period may change substantially in value (e.g., ripen or spoil). Consequently, when selecting food for a long-term cache, an animal should consider what the value of each food item will be when it is eaten rather than when it is collected. This point adds considerable complexity to the problem of food selection compared with the situation addressed by most prey choice models. Beginning with the premise that an animal should store no more of a food type than can be consumed before the remainder spoils, we developed a numerical computer simulation to evaluate three cache management strategies under various conditions of food availability and duration of the cache use period. On the basis of deterioration rates, the simulation predicts how much of each food type an animal should store. The results indicate that animals should adjust the composition of their cache to reflect food perishability and that no one inventory strategy is optimal under all conditions.
Neighborhood-Level Chronic Disease Surveillance: Utility of Primary Care Electronic Health Records and Emergency Department Claims Data

Supplemental Digital Content is Available in the Text. Context: Disease burden may vary substantively across neighborhoods in an urban setting. Yet, data available for monitoring chronic conditions at the neighborhood level are scarce. Large health care data sets have potential to complement population health surveillance. Few studies have examined the utility of health care data for neighborhood-level surveillance. Objective: We examined the use of primary care electronic health records (EHRs) and emergency department (ED) claims for identifying neighborhoods with higher chronic disease burden and neighborhood-level prevalence estimation. Design: Comparison of hypertension and diabetes estimates from EHRs and ED claims with survey-based estimates. Setting: Forty-two United Hospital Fund neighborhoods in New York City. Participants: The EHR sample comprised 708 452 patients from the Hub Population Health System (the Hub) in 2015, and the ED claim sample comprised 1 567 870 patients from the Statewide Planning and Research Cooperative System in 2015. We derived survey-based estimates from 2012 to 2016 Community Health Survey (n = 44 189). Main Outcome Measure: We calculated hypertension and diabetes prevalence estimates by neighborhood from each data source. We obtained Pearson correlation and absolute difference between EHR-based or claims-based estimates and survey-based estimates. Results: Both EHR-based and claims-based estimates correlated strongly with survey-based estimates for hypertension (0.91 and 0.72, respectively) and diabetes (0.83 and 0.82, respectively) and identified similar neighborhoods of higher burden. For hypertension, 10 and 17 neighborhoods from the EHRs and ED claims, respectively, had an absolute difference of more than 5 percentage points from the survey-based estimate. For diabetes, 15 and 4 neighborhoods from the EHRs and ED claims, respectively, differed from the survey-based estimate by more than 5 percentage points. Conclusions: Both EHRs and ED claims data are useful for identifying neighborhoods with greater disease burden and have potential for monitoring chronic conditions at the neighborhood level.
Clinical management of tendinopathy: A systematic review of systematic reviews evaluating the effectiveness of tendinopathy treatments

While the pathoetiology is disputed, a wide array of treatments is available to treat tendinopathy. The most common treatments found in the literature include therapeutic modalities, exercise protocols, and surgical interventions; however, their effectiveness remains ambiguous. The purpose of this study was to perform a systematic review of systematic reviews to determine the ability of therapeutic interventions to improve pain and dysfunction in patients with tendinopathy regardless of type or location. Five databases were searched for systematic reviews containing only randomized control trials to determine the effectiveness of treatments for tendinopathies based on pain and patient‐reported outcomes. Systematic reviews were assessed via the Assessment of Multiple Systematic Reviews (AMSTAR) for methodological quality. From the database search, 3,295 articles were found, 107 passed the initial inclusion criteria. After further review, 25 systematic reviews were included in the final qualitative analysis. The AMSTAR scores were relatively high (8.8 ± 1.0) across the 25 systematic reviews. Eccentric exercises were the most common and consistently effective treatment for tendinopathy across systematic reviews. Low‐level laser therapy and extracorporeal shockwave therapy demonstrated moderate effectiveness, while platelet‐rich plasma injections demonstrated inconclusive evidence on their ability to decrease tendinopathy‐related pain and improve function. Corticosteroids also showed some effectiveness for short‐term pain, but for the long‐term use deemed ineffective and at times contraindicated. Regarding surgical options, minimally invasive procedures were more effective compared to open surgical interventions. When treating tendinopathy regardless of location, eccentric exercises were the best treatment option to improve tendinopathy‐related pain and improve self‐reported function.
Changes in Habitat and Microhabitat Partitioning within an Assemblage of Stream Fishes in Response to Predation by Sacramento Squawfish (Ptychocheilus grandis)

The Sacramento squawfish (Ptychocheilus grandis), a piscivorous cyprinid, was recently (ca. 1979) introduced into the Eel River, California, USA. We compared habitat and microhabitat use of resident fishes between areas where squawfish were present and absent at one location and between years before and after invasion by squawfish at a second location. The resident species showed a variety of responses to the presence of the predator. Juvenile rainbow trout (Oncorhynchus mykiss) and juvenile Sacramento suckers (Catostomus occidentalis) increased their use of fast-flowing riffles at both locations, in the presence of squawfish. Suckers also used significantly shallower depths within habitat types. Adult California roach (Lavinia symmetricus) decreased their use of run habitat and increased use of pools and riffles at the first site, but not at the second. When squawfish were present, juvenile roach and threespine stickleback (Casterosteus aculeatus) were found in shallower water closer to the stream edge i.
Effect of lead poisoning on spectacled eider survival rates

Spectacled eider (Somateria fischeri) populations on the Yukon-Kuskokwim Delta (Y-K Delta), Alaska, declined rapidly through the 1980s, and low adult female survival was suggested as the likely cause of the decline. We used mark-resighting techniques to study annual survival rates of adult female spectacled eiders at 2 sites on the Y-K Delta during 1993-96. Our data suggest survival rates may differ among sites. However, a model fit to a subset of data on females for which we knew lead levels in blood suggests lead exposure influences survival. Adult females exposed to lead prior to hatching their eggs survived at a much lower rate (0.44 ± 0.10) each year than females not exposed to lead before hatch (0.78 ± 0.05). We suggest most mortality from lead exposure occurs over winter, and the related reduction in adult survival may be impeding recovery of local populations. We encourage managers to curtail input of lead shot into the environment.
Lactic acid in cancer and mitochondrial disease

Cancer and the mitochondrial diseases are disparate disorders that have in common a failure of normal cellular respiratory activity in disease‐affected tissues. In mitochondrial diseases, the impairment in the mitochondria is often the result of abnormalities in their mtDNA, whereas in cancerous cells, the altered respiration is driven by the Warburg effect. The oxidation of glucose (as pyruvate in the mitochondria) is inhibited and energy production relies on cytoplasmic glycolysis. This suppressed mitochondrial activity confers in tumor cells a state of resistance to apoptosis and, in mitochondrial diseases like mitochondrial encephalopathy, lactic acidosis, and stroke‐like episodes (MELAS), the altered respiration leads to lactic acidosis. Driving glucose to its complete oxidation inside the mitochondria has potential in cancer therapy to reconstitute apoptotic competence in tumor cells and, in mitochondrial disease, to treat lactic acidosis. This minireview investigates the development of small molecule agents for suppressing the Warburg effect in cancer therapy and lactic acidosis in mitochondrial disease. Drug Dev Res 70:499–511, 2009. © 2009 Wiley‐Liss, Inc.
Neoadjuvant Treatment for Triple Negative Breast Cancer: Recent Progresses and Challenges

Triple negative breast cancer (TNBC) is an aggressive breast cancer with historically poor outcomes, primarily due to the lack of effective targeted therapies. The tumor molecular heterogeneity of TNBC has been well recognized, yet molecular subtype driven therapy remains lacking. While neoadjuvant anthracycline and taxane-based chemotherapy remains the standard of care for early stage TNBC, the optimal chemotherapy regimen is debatable. The addition of carboplatin to anthracycline, cyclophosphamide, and taxane (ACT) regimen is associated with improved complete pathologic response (pCR). Immune checkpoint inhibitor (ICI) combinations significantly increase pCR in TNBC. Increased tumor infiltrating lymphocyte (TILs) or the presence of DNA repair deficiency (DRD) mutation is associated with increased pCR. Other targets, such as poly-ADP-ribosyl polymerase inhibitors (PARPi) and Phosphatidylinositol-3-kinase/Protein Kinase B/mammalian target of rapamycin (PI3K-AKT-mTOR) pathway inhibitors, are being evaluated in the neoadjuvant setting. This review examines recent progress in neoadjuvant therapy of TNBC, including platinum, ICI, PARPi, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) pathway targeted therapies, and novel tumor microenvironment (TME) targeted therapy, in addition to biomarkers for the prediction of pCR.
Diabetes Prevention for Pacific People in the United States: A Mixed-Methods Feasibility Study to Adapt the Diabetes Prevention Program With Samoan/Tongan Church Communities

Objective: To determine baseline characteristics of a group of Samoans/Tongans in Southern California at risk for type 2 diabetes mellitus and identify barriers, cultural factors, and readiness and capacity to implement a culturally tailored Diabetes Prevention Program (DPP) in a faith-based setting. Design: A mixed-methods pilot that included piloting modified DPP sessions, conducting a survey, and focus groups (N = 4). Setting: Samoan/Tongan faith-based organizations. Participants: Samoan/Tongan church members in Southern California who were interested in lifestyle behavior change. Main Outcome Measures: Surveys assessing sociodemographic, acculturation, health status, food insecurity, and psychosocial factors. Focus groups focusing on attitudes toward the curriculum, opportunities for tailoring, and specific barriers/facilitators for healthy weight, nutrition, and physical activity. Results: Participants (N = 47) were on average 42 years old, female (57%), and identified as Pacific Islander (35% Samoan, 30% American Samoan, and 35% Tongan). Ninety-eight percent of respondents were overweight/obese, and 45% of households were food insecure. Less than half of respondents were born in the United States, and 28% reported “poor” or “fair” English proficiency. Those with higher body mass indexes were more likely to score lower on internal locus of control and self-efficacy for healthy eating and were motivated to lose weight to feel in control of their health. Focus group results revealed that members of the Samoan/Tongan communities are “underserved” and experience a lack of culturally relevant programs to address obesity and chronic disease. Several barriers to healthier lifestyles were identified including adaptation of traditional recipes made in the United States (ie, to be less healthy), role of stress, cultural values (eg, preference for larger body size), and lack of awareness about healthy lifestyles. The church was identified as a resource that could be leveraged further to positively impact health outcomes. Conclusions: Results demonstrate possible ways to tailor the DPP for US-based Samoan/Tongan populations by harnessing cultural traditions and addressing existing barriers and psychosocial constructs.