Miracle-dz/UniFAR-FTUs huggingface dataset:
Chloroplast 16S rDNA Sequences and Phylogenetic Relationships of Fern Allies and Ferns

Chloroplast 16S rDNA sequences from the charophyte algae Spirogyra and Coleo- chaete; the bryophytes Marchantia and Sphagnum; the fern allies Equisetum, Isoetes, Selaginella, Lycopodium, Tmesipteris and Psilotum; the eusporangiate ferns Angiopteris, Botrychium, and Ophioglossum; the leptosporangiate ferns Lydogium and Doodia; the gymnosperms Ephedra and Juniperus; and six angiosperms (two monocots and four dicots) were analyzed with the parsimony algorithm PAUP to infer phylogenetic relationships. The charophytes were the designated out- group and the bryophytes were at the base of the land plant clade. Relationships of most of the fern allies and Angiopteris were unresolved but a clade containing Psilotum + Tmesipteris (Psi- lotales) was sister to a clade composed of Botrychium and Ophioglossum (Ophioglossales). A leptosporangiate fern clade was strongly supported, and this clade grouped weakly with Angiop- teris. The Selaginella 16S rDNA sequence is apparently changing at a faster rate than the other sequences as evidenced by the extremely long branch associated with Selaginella. The effect of this long branch on the overall tree topology was tested by removing Selaginella from a subsequent analysis. Trees produced without Selaginella weakly supported the placement of Lycopodium at the base of the vascular plants clade but Isoetes grouped weakly with the seed plants. Removal of Selaginella also resulted in higher bootstrap values and decay indices for the majority of the clades. The determination of phylogenetic relationships of the "fern allies," the Psi- lophyta, Lycophyta, and Sphenophyta, has proven to be elusive. Taxonomi- cally, the fern allies are generally considered to be positioned between the bryophytes and ferns but formal analyses of morphological and molecular data sets only partially resolve their relationships. In a cladistic analysis of mor- phological characters, Bremer et al. (1987) placed Psilotum at the base of vas- cular plants, the lycopsids branched off next, then Equisetum, and then the ferns. However, the portion of the clade containing the fern allies was con- structed with only four morphological characters and it is not reasonable to expect that a robust phylogeny containing highly divergent taxa can be pro- duced from such a small data set. Conversely, fossil evidence (Knoll and Roth- well, 1981; Stewart, 1983; Gensel and Andrews, 1984), characters relating to male gametogenesis (Garbary et. al., 1993), and chloroplast genome structures (Raubeson and Jansen, 1992) support the hypothesis that the lycophytes are at the base of the vascular land plant clade. Mishler et al. (1994) analyzed green plant molecular and morphological data sets separately and together, using parsimony algorithms. Some vascular land plants were included, with the fern allies represented by Equisetum, Lycopo- dium, Lycopodiella, and Selaginella. The analysis of "general" morphological characters placed the lycophytes sister to a clade containing Equisetum, ferns,
Semiparametric Estimation of the Random Utility Model with Rank- Ordered Choice Data

We propose two semiparametric methods for estimating the random utility model using rank-ordered choice data. The framework is “semiparametric” in that the utility index includes finite dimensional preference parameters but the error term follows an unspecified distribution. Our methods allow for a flexible form of heteroskedasticity across individuals. With complete preference rankings, our methods also allow for heteroskedastic and correlated errors across alternatives, as well as a variety of random coefficients distributions. The baseline method we develop is the generalized maximum score (GMS) estimator, which is strongly consistent but follows a non-standard asymptotic distribution. To facilitate statistical inferences, we make extra regularity assumptions and develop the smoothed GMS estimator, which is asymptotically normal. Monte Carlo experiments show that our estimators perform favorably against popular parametric estimators under a variety of stochastic specifications.
Mating frequencies of Africanized honey bees in the south western USA

Summary Emerging evidence suggests that there are significant adaptive advantages conferred to genetically diverse honey bee colonies through multiple matings with queens. We determined the intracolony genetic diversity of Africanized honey bee (AHB) colonies from a feral population in the south western USA. A total of 1,253 worker offspring were genotyped from 20 feral colonies (all but three of African mitotype), four managed AHB, three managed European honey bee (EHB), and four control colonies (headed by EHB queens instrumentally inseminated with one, two, five, or ten drones, respectively) using eight microsatellite markers. The 17 feral AHB queens mated with an average of 20.0 ± 6.53 (range 10–32) drones, resulting in effective paternity frequencies of 20.0 ± 8.46 (range 10.56–37.53), which is one of the highest mating numbers recorded within the species. Though Africanized honey bee colonies are among the most genetically diverse Apis mellifera yet recorded, their queen mating frequencies are within the expected range of the species overall, including African honey bees in their native range. The factors responsible for these findings are discussed.
The prognostic value of neutrophil gelatinase-associated lipocalin in sepsis-associated acute kidney injury: A prospective observational study

Background: Sepsis is one of the most common triggering factors for acute kidney injury (AKI). The aim of the study is to evaluate the outcome in sepsis with AKI and determine the prognostic value of urinary neutrophil gelatinase-associated lipocalin (NGAL) in septicemic AKI. Materials and Methods: This prospective follow-up study was carried out over a period of 1 year after ethical clearance from the Institutional Ethics committee, a total 165 cases of septicemia were recruited, of which 15 patients were dropped out, 150 patients were identified suffering from septicemia defined as per the organ dysfunction criteria (according to third international consensus 2016) and patients of AKI defined as per the Kidney Disease Improving Global Outcomes 2012 criteria). Results: Out of 150 patients of septicemia enrolled in the study, only 38 (25.33%) suffering from AKI were classified as Group I and rest 112 (74.67%) patients of septicemia not suffering from AKI were classified as Group II. In total, 60.0% (90) patients were discharged from the hospital, rest of the patients (40%) expired. Mean duration of survival was higher in Group II (21.29 ± 1.89 days) as compared to Group I (13.67 ± 1.06 days). Cases with ≥121.90 urine NGAL, rate of mortality (41.7%), were higher as compared to alive patients discharged (34.4%). Conclusion: Sequential organ failure assessment score, hospital stay, and mortality were high in septicemic patients with AKI as compared to sepsis without AKI. Survival of patients also not good with septic AKI, those patients who had high NGAL value had poor prognosis.
Progress in the pathogenesis of thyroid-associated ophthalmopathy and new drug development

Thyroid-associated ophthalmopathy (TAO) is the most common extrathyroidal manifestation of toxic diffuse goiter (Graves' disease), also known as Graves' ophthalmopathy/orbitopathy. As an organ-specific autoimmune disease, the pathogenesis of TAO is still unclear. In recent years, great progress has been made in revealing the mechanism of TAO. Various biological and immunosuppressive agents have emerged in an endless stream, showing encouraging results. Strengthening the basic research, establishing ideal animal models, deeply understanding the pathogenesis, and developing novel targeted drugs are of great significance to guide the clinical diagnosis and management of TAO and improve the prognosis of patients.
Impact of critical care response team implementation on oncology patient outcomes: A retrospective cohort study

Introduction: The main goal of a critical care response team (CCRT) is to quickly assess and transfer, if required, rapidly deteriorating patients to an intensive care unit (ICU) to prevent cardiopulmonary arrest, stabilize patients' condition, and help in optimizing the care provided by the primary team. The objective of this study was to investigate the correlation between early intervention by CCRT and the outcome of oncology patients. Materials and Methods: This is a retrospective cohort study conducted at King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. KAMC is a tertiary care facility with 1200-bed capacity. The study compared oncology patients to nononcology patients. Results: Over 4 years, a total number of 4941 patients were reviewed, of which 172 were oncology patients. The average age of patients in the oncology group was 48.8 ± 20.7, while the average age for nononcology was 52.8 ± 21.2 (P = 0.016). The average Acute Physiology and Chronic Health Evaluation II score on admission for oncology patients was higher than that for the nononcology group (27.8 ± 8.9 vs. 23.6 ± 9.3, respectively). Lower ICU mortality was seen after CCRT implementation (38.8% vs. 62.7%). The average duration of hospital stay and ICU stay increased after CCRT implementation (37.34 vs. 29.31 and 11.93 vs. 8.9, respectively). Conclusion: In this study, we identified that early intervention by implementing CCRT had a significant impact in reducing ICU mortality for oncology and nononcology patients.
Variability in Current Trauma Systems and Outcomes

Background: Complication rates may be indicative of trauma center (TC) performance. The complication rates between Level 1 and 2 TCs at the national level are unknown. Our study aimed to determine the relationship between American College of Surgeons (ACS)-verified and state-designated TCs and complications. Study Design and Methods: This was a cohort review of the National Sample Program (NSP) from the National Trauma Data Bank, the world's largest validated trauma database. TCs were categorized by ACS or state Level 1 or 2. TCs not categorized as Level 1 or 2 were excluded. All 22 complications provided by the NSP were analyzed. Chi-squared analysis was used with statistical significance defined asP < 0.05. Results: Of the 94 TCs in the NSP, 67 had ACS and 80 had state designations of Level 1 or 2. There were 38 ACS Level 1 TCs treating 87,340 patients and 29 ACS Level 2 TCs treating 35,763. There were 45 state Level 1 TCs treating 106,640 and 35 state Level 2 TCs treating 43,290. ACS Level 1 TCs had significantly higher complications compared to ACS Level 2 TCs (13.5% [11,776/87,340] vs. 10.1% [3,606/35,763],P < 0.0001). In addition, state Level 1 TCs had significantly more complications compared to state Level 2 TCs (4.4% [4,681/106,640] vs. 1.6% [673/43,290],P < 0.0001). Conclusion: Both ACS and state Level 2 TCs had significantly lower complication rates than ACS and state Level 1 TCs. Further investigations should look for the source and impact of this difference.
New insight into the effect of lycopene on the oxidative stress in acute kidney injury

Objective: To evaluate the nephroprotective effect of lycopene (LPN) in acute kidney injury (AKI) regarding the oxidative stress (OS). Materials and Methods: Thirty Sprague Dawley male rats were divided into three groups – control group: rats treated with distilled water (orally) for 10 days (n = 10); AKI group: rats treated with distilled water and diclofenac (intraperitoneal) for 10 days (n = 10); treated group: rats treated with LPN (orally) and diclofenac for 10 days (n = 10). Body mass index (BMI) and estimated glomerular filtration rate (eGFR) were measured. Blood urea, serum creatinine (CreSerum), serum malondialdehyde (MDA), superoxide dismutase (SOD), neutrophil gelatinase-associated lipocalin (NGAL), and kidney injury molecules (KIM-1) were measured in the all groups on the 11th day of the experiment. Results: Diclofenac-induced AKI led to significant elevations of BMI, CreSerum, and blood urea compared with control (P < 0.05). In AKI model, eGFR was reduced to 11.69 ± 2.64 ml/min/1.73 compared with control group (15.88 ± 3.75 ml/min/1.73, P = 0.03). NGAL, MDA, and KIM-1 were elevated in AKI compared with control (P < 0.001). Pretreatment with LPN led to the reduction of blood urea and CreSerum as compared with AKI (P < 0.001). Similarly, eGFR was increased significantly to 14.81 ± 3.21 ml/min/1.73 compared with 11.69 ± 2.64 ml/min/1.73 in AKI (P = 0.02). Serum levels of NGAL, KIM-1, and MDA were reduced significantly in the LPN group as compared with AKI (P = 0.001), while the SOD serum level was increased to 33. 86 ± 8.61 pg/ml as compared to 22.78 ± 7.56 pg/ml in AKI (P = 0.006). As well, LPN reduced MDA/SOD ratio as compared with AKI (P = 0.00001). Conclusion: The finding of this study illustrated that LPN is an effective natural antioxidant that attenuates and prevents AKI through modulation of OS and lipid peroxidation. As well, LPN might be of great value in the prevention of nephrotoxicity that induced by nephrotoxic agents like diclofenac.
Absence of a pelagic phase in the life cycle of the flatback turtle, Natator depressa (Garman)

Prey remnants at island feeding stations of the white-bellied sea-eagle Haliaeetus leucogaster (Gmelin) were examined along the Great Barrier Reef. Juvenile flatback turtles Natator depressa (Garman) 14-24cm in shell length were preyed upon primarily within the main feeding and nesting range of adult turtles. There was no evidence of predation on the juveniles of other species of sea-turtles which are reported to inhabit oceanic environ-
Listeria in Seafoods: A Review.

Listeria is an environmental contaminant which has been isolated from marine and fresh waters, as well as various seafoods. Furthermore, Listeria , including Listeria monocytogenes , has been isolated from processed seafood products such as smoked fish, cooked and frozen seafoods, marinated fish, surimi products, etc. The pathogen, L. monocytogenes , does have a certain degree of heat resistance. It was found to survive in internally infected shrimp after boiled for up to 5 min. However, the commercial pasteurization process for crab meat was found to be sufficient to inactivate Listeria . The current recovery methodology for L. monocytogenes from seafoods is the Food and Drug Administration Listeria protocol.
Postharvest Dip in a Natural Lipid, Lysophosphatidylethanolamine, May Prolong Vase Life of Snapdragon Flowers

We investigated the use of lysophosphatidylethanolamine (LPE) for prolonging vase life of snapdragon (Antirrhinum majus L.). Freshly cut snapdragon spikes were set into a LPE solution at 25 mg.L -1 for 24 h and then transferred to deionized water. The vase life was enhanced by LPE. The flowers on spikes treated with LPE showed symptoms of wilting or browning 4 or 6 days later than those on the spikes given deionized water in inbred or 'Potomac White', respectively. All the spikes were of marketable quality for 5 to 7 days after harvest when treated with LPE, whereas in the control only about half of the flowers were of marketable quality at 2 days after harvest. LPE treatment also delayed fresh mass loss, lowered endogenous ethylene production, and reduced ion leakage. These results suggest that LPE has commercial potential in enhancing vase life of snapdragons.
Tracking Calcium Dynamics and Immune Surveillance at the Choroid Plexus Blood-Cerebrospinal Fluid Interface

The choroid plexus (ChP) epithelium is a source of secreted signaling factors in cerebrospinal fluid (CSF) and a key barrier between blood and brain. Here, we develop imaging tools to interrogate these functions in adult lateral ventricle ChP in whole-mount explants and in awake mice. By imaging epithelial cells in intact ChP explants, we observed calcium activity and secretory events that increased in frequency following delivery of serotonergic agonists. Using chronic two-photon imaging in awake mice, we observed spontaneous subcellular calcium events as well as strong agonist-evoked calcium activation and cytoplasmic secretion into CSF. Three-dimensional imaging of motility and mobility of multiple types of ChP immune cells at baseline and following immune challenge or focal injury revealed a range of surveillance and defensive behaviors. Together, these tools should help illuminate the diverse functions of this understudied body-brain interface.
Graphs, spanning trees and divergence-free finite elements in general topological domains

We construct sets of basis functions of the space of divergence-free finite elements of Raviart–Thomas type in a general topological domain. Two different methods are presented: one using a suitable selection of the curls of Nédélec finite elements, the other based on an efficient algebraic procedure. The first approach looks to be more useful for numerical approximation, as the basis functions have a localized support.
Review of QTL mapping results in chickens

A review of QTL for production, behaviour and disease resistance traits published to the end of 2004 is presented. QTL were located randomly over the genome and there was little commonality between different studies for similar traits. However, there were several reports of QTL from different experiments in similar regions of chromosomes 1 (at 250 and 450 cM), 4 and 8 and for disease resistance on chromosome 5. Generally there were 6 to 8 QTL affecting the major production traits in experimental breed crosses and collectively they accounted for a substantial proportion of the line difference where this information was provided. The size of typical genome-wide significant effects for production traits was 0.3 to 1.0 phenotypic standard deviations. Genetic effects for growth traits were generally additive whereas about one-third of QTL for other production traits showed significant dominance effects. Variable reporting standards were noted and proposals for minimum published information are presented. Currently there are scientific opportunities for meta-analyses of results from experiments on body weight gain and considerable potential for combining data and results from different studies for other traits in the future.
Nutrient Losses from Sandy Soils during Old-field Succession

Since the cessation of farming in 1951, concentrations of available P and exchangeable Ca have declined in the Ap horizons of the sandy soils of the Savannah River Plant, located near Aiken, South Carolina. During the 1st 10 years of succession, P and Ca concentrations declined rapidly. Subsequently, P concentrations have changed little, if at all, whereas Ca concentrations have continued to decrease, at least in some soils. Exchangeable K concentrations decreased by 50 o in Eustis soils but have changed little in Lakeland or Fuquay soils. Nutrients lost from the Ap horizons (i.e., the top 15 cm) do not appear to have been retained in the upper 1 m of the soil.
Keep an eye on acute optic neuropathy

151 G blind after recovery from general anesthesia in patients who undergo spinal fusion is a catastrophic event. Perioperative visual loss (POVL) is most commonly due to ischemic optic neuropathy (ION), followed by retinal arterial occlusion. [1] The first description of POVL in Medline, named “Postoperative amaurosis,” was published in 1950. [2] Along with the rapid growth in spine procedures, the yearly number of POVL publications accelerated dramatically. [3] However, the number of cases reported POVL registry yearly has been decreasing from a peak in 2000 and has been dropping since. [4] Peri‐operative ION (PO‐ION) in spine fusion decreased statistically significantly (P = 0.002) from 1.63/10,000 in 1998 to 0.60/10,000 in 2010. [1] This seems a great news to us, but why is the incidence of PO‐ION falling? It is probably due to a reduction in operative times along with intraoperative blood transfusion. [4]
The effect of the body mass index on the short-term surgical outcomes of laparoscopic total gastrectomy: A propensity score-matched study

Purpose: This study aimed to evaluate the relationship between the body mass index (BMI) and the short-term outcomes of laparoscopic total gastrectomy (LTG). Subjects and Methods: Data of patients who underwent LTG for gastric cancer at six institutions between 2004 and 2018 were retrospectively collected. The patients were classified into three groups: low BMI (<18.5 kg/m2), normal BMI (≥18.5 and <25 kg/m2) and high BMI (≥25 kg/m2). In these patients, clinicopathological variables were analysed using propensity score matching for age, sex, the American Society of Anaesthesiologists physical state, clinical stage, surgical method, D2 lymph node dissection, combined resection of other organs, anastomosis method and jejunal pouch reconstruction. The surgical results and post-operative outcomes were compared among the three groups. Results: A total of 82 patients were matched in the analysis of the low BMI and normal BMI groups. There were no differences in operative time (P = 0.693), blood loss (P = 0.150), post-operative complication (P = 0.762) and post-operative hospital stay (P = 0.448). In the analysis of the normal BMI and high BMI groups, 208 patients were matched. There were also no differences in blood loss (P = 0.377), post-operative complication (P = 0.249) and post-operative hospital stay (P = 0.676). However, the operative time was significantly longer in the high BMI group (P = 0.023). Conclusions: Despite the association with a longer operative time in the high BMI group, BMI had no significant effect on the surgical outcomes of LTG. LTG could be performed safely regardless of BMI.
Clinico-demographic profile & hospital outcomes of COVID-19 patients admitted at a tertiary care centre in north India

Background & objectives: In December 2019, a novel coronavirus (SARS-CoV-2) emerged in China and rapidly spread globally including India. The characteristic clinical observations and outcomes of this disease (COVID-19) have been reported from different countries. The present study was aimed to describe the clinico-demographic characteristics and in-hospital outcomes of a group of COVID-19 patients in north India. Methods: This was a prospective, single-centre collection of data regarding epidemiological, demographic, clinical and laboratory parameters, management and outcome of COVID-19 patients admitted in a tertiary care facility in north India. Patient outcomes were recorded as death, discharge and still admitted. Results: Data of 144 patients with COVID-19 were recorded and analyzed. The mean age of the patients was 40.1±13.1 yr, with 93.1 per cent males, and included 10 (6.9%) foreign nationals. Domestic travel to or from affected States (77.1%) and close contact with COVID-19 patients in congregations (82.6%) constituted the most commonly documented exposure. Nine (6.3%) patients were smokers, with a median smoking index of 200. Comorbidities were present in 23 (15.9%) patients, of which diabetes mellitus (n=16; 11.1%) was the most common. A significant proportion of patients had no symptoms (n=64; 44.4%); among the symptomatic, cough (34.7%) was the most common symptom followed by fever (17.4%) and nasal symptoms (2.15%). Majority of the patients were managed with supportive treatment with hydroxychloroquine and azithromycin given on a case-to-case basis. Only five (3.5%) patients required oxygen supplementation, four (2.8%) patients had severe disease requiring intensive care, one required mechanical ventilation and mortality occurred in two (1.4%) patients. The time to reverse transcription-polymerase chain reaction (RT-PCR) negativity was 16-18 days. Interpretation & conclusions: In this single-centre study of 144 hospitalized patients with confirmed COVID-19 in north India, the characteristic findings included younger age, high proportion of asymptomatic patients, long time to PCR negativity and low need for intensive care unit care.