Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimates of age and growth in a population of green sea turtles (Chelonia mydas) from the Indian River lagoon system, Florida: a skeletochronological analysis

The Indian River lagoon system harbors a dynamic population of juvenile green sea turtles (Chelonia mydas). This foraging or developmental population occupies the lagoon year-round and periodically experiences cold-stunning events that kill a portion of the population. A sample of 59 C. mydas (28-74 cm straight carapace length) from the December 1989 cold-stunning event was aged by skeletochronology, yielding age estimates of 3-14 years. Mean growth-rate estimates range from 30 to 52 mm/year for most age and size classes, with means for the 6- to 11-year age classes (44-49 mm/year) not significantly different but greater than those of the youngest and oldest classes (3-5 and 12 years old, respectively) (32-38 mm/year). Because of the lack of adults and near-adults in the sample, growth models (e.g., Gompertz) do not yield biologically realistic asymptotes, hence they do not provide accurate estimates of age at sexual maturity. The age estimates suggest that the western Atlantic C. mydas change from a pela.
Conservation on community lands: the importance of equitable revenue sharing

SUMMARY Attempts to establish local support for wildlife and conservation through the sharing of revenues and empowerment of local communities to manage their wildlife have proliferated over the past two decades. Data from two neighbouring Maasai group ranches in the wildlife dispersal area of Amboseli and Tsavo National Parks (Kenya) indicated one ranch generated considerable wildlife revenues from a tourist operation and community trust while the other received no direct benefits from wildlife. The overall attitude to wildlife on the ranch with wildlife revenues was significantly more positive, but attitudes within the ranch varied significantly, depending on both costs from wildlife and perception of the distribution of wildlife revenues. Ordinal logistic regression analyses showed that it was not the amount of revenue received or the scale of costs from wildlife which determined people's attitudes, but simply the presence or absence of wildlife benefits. The importance of addressing inequitable distribution of benefits is emphasized.
Primary EUS-guided biliary drainage versus ERCP drainage for the management of malignant biliary obstruction: A systematic review and meta-analysis

EUS-guided biliary drainage (EUS-BD) has been used as a salvage modality for relief of malignant biliary obstruction (MBO) after a failed ERCP. Multiple recent randomized controlled trials (RCTs) and observational studies have been published to assess the suitability of EUS-BD as a first-line modality for achieving palliative BD. We aimed to perform a systematic review and meta-analysis comparing primary EUS-BD versus ERCP for MBO. We searched PubMed, Medline, and Embase up to January 1, 2019, to identify RCTs and observational studies evaluating the efficacy and safety of primary EUS-BD (without a prior attempted ERCP) versus ERCP. Quality of RCTs and observational studies was assessed using Jadad and Newcastle–Ottawa scores, respectively. The outcomes of interest were technical success, clinical success, odds of requiring a repeat intervention, and procedure-related adverse events. Odds ratios (ORs) and standard mean difference were calculated for categorical and continuous variables, respectively. Meta-analysis was performed using the random effects model in RevMan 5.3 (the Cochrane Collaboration, the Nordic Cochrane Centre, Copenhagen, Denmark). Five studies (three RCTs and two observational studies) with 361 patients were included. Both procedures achieved comparable technical success (OR: 1.20 [0.44–3.24], I2 = 0%) and clinical success (OR: 1.44, confidence interval [CI]: 0.63–3.29, I2 = 0%). The overall adverse outcomes (OR: 1.59 [0.89–2.84]) did not differ between the two groups. In the ERCP group, 9.5% of patients developed procedure-related pancreatitis versus zero in the EUS group (risk difference = 0.08%, P = 0.02). There was no statistically significant difference in nonpancreatitis-related adverse events. The odds of requiring reintervention for BD (1.68 [0.76–3.73], I2 = 42%) did not differ significantly. The ERCP group had significantly higher odds of requiring reintervention due to tumor overgrowth (5.35 [1.64–17.50], I2 = 0%). EUS-BD has comparable technical and clinical success to ERCP and can potentially be used as a first-line palliative modality for MBO where expertise is available. ERCP-related pancreatitis which can cause significant morbidity can be completely avoided with EUS.
Mortality, causes of death and influence of medication use in patients with systemic lupus erythematosus vs matched controls

Abstract Objectives We wanted to estimate the magnitude of the risk from all-cause, cause-specific and sex-specific mortality in patients with SLE and relative risks compared with matched controls and to evaluate the influence of exposure to medication on risk of mortality in SLE. Methods We conducted a population-based cohort study using the Clinical Practice Research Datalink, Hospital Episode Statistics and national death certificates (from 1987 to 2012). Each SLE patient (n = 4343) was matched with up to six controls (n = 21 780) by age and sex. Cox proportional hazards models were used to estimate overall and cause-specific mortality rate ratios. Results Patients with SLE had a 1.8-fold increased mortality rate for all-cause mortality compared with age- and sex-matched subjects [adjusted hazard ratio (HR) = 1.80, 95% CI: 1.57, 2.08]. The HR was highest in patients aged 18–39 years (adjusted HR = 4.87, 95% CI: 1.93, 12.3). Mortality rates were not significantly different between male and female patients. Cumulative glucocorticoid use raised the mortality rate, whereas the HR was reduced by 45% with cumulative low-dose HCQ use. Patients with SLE had increased cause-specific mortality rates for cardiovascular disease, infections, non-infectious respiratory disease and for death attributable to accidents or suicide, whereas the mortality rate for cancer was reduced in comparison to controls. Conclusion British patients with SLE had a 1.8-fold increased mortality rate compared with the general population. Glucocorticoid use and being diagnosed at a younger age were associated with an increased risk of mortality. HCQ use significantly reduced the mortality rate, but this association was found only in the lowest cumulative dosage exposure group.
Automated gap-filling for marker-based biomechanical motion capture data

Abstract Marker-based motion capture presents the problem of gaps, which are traditionally processed using motion capture software, requiring intensive manual input. We propose and study an automated method of gap-filling that uses inverse kinematics (IK) to close the loop of an iterative process to minimize error, while nearly eliminating user input. Comparing our method to manual gap-filling, we observe a 21% reduction in the worst-case gap-filling error (p < 0.05), and an 80% reduction in completion time (p < 0.01). Our contribution encompasses the release of an open-source repository of the method and interaction with OpenSim.
Distinctive alteration in the expression of autophagy genes in Drosophila models of amyloidopathy and tauopathy

Abstract Background Alzheimer’s disease (AD) is one the most common types of dementia. Plaques of amyloid beta and neurofibrillary tangles of tau are two major hallmarks of AD. Metabolism of these two proteins, in part, depends on autophagy pathways. Autophagy dysfunction and protein aggregation in AD may be involved in a vicious circle. The aim of this study was to investigate whether tau or amyloid beta 42 (Aβ42) could affect expression of autophagy genes, and whether they exert their effects in the same way or not. Methods Expression levels of some autophagy genes, Hook, Atg6, Atg8, and Cathepsin D, were measured using quantitative PCR in transgenic Drosophila melanogaster expressing either Aβ42 or Tau R406W. Results We found that Hook mRNA levels were downregulated in Aβ42-expressing flies both 5 and 25 days old, while they were increased in 25-day-old flies expressing Tau R406W. Both Atg6 and Atg8 were upregulated at day 5 and then downregulated in 25-day-old flies expressing either Aβ42 or Tau R406W. Cathepsin D expression levels were significantly increased in 5-day-old flies expressing Tau R406W, while there was no significant change in the expression levels of this gene in 5-day-old flies expressing Aβ42. Expression levels of Cathepsin D were significantly decreased in 25-day-old transgenic flies expressing Tau R406W or Aβ42. Conclusion We conclude that both Aβ42 and Tau R406W may affect autophagy through dysregulation of autophagy genes. Interestingly, it seems that these pathological proteins exert their toxic effects on autophagy through different pathways and independently.
Quantifying Factors Essential to the Integrity of the Esophagogastric Junction During Antireflux Procedures

Objective: To quantify the contribution of key steps in antireflux surgery on compliance of the EGJ. Background: The lower esophageal sphincter and crural diaphragm constitute the intrinsic and extrinsic sphincters of the EGJ, respectively. Interventions to treat reflux attempt to restore the integrity of the EGJ. However, there are limited data on the relative contribution of critical steps during antireflux procedures to the functional integrity of the EGJ. Methods: Primary antireflux surgery was performed on 100 consecutive patients with pathologic reflux. Intraoperative EGJ measurements including distensibility index (DI), cross-sectional area (CSA), and HPZ length were collected using EndoFLIP. Data was acquired pre-repair, post-diaphragmatic re-approximation with sub-diaphragmatic EGJ relocation, and post-sphincter augmentation. Results: Patients underwent Nissen (45%), Toupet (44%), or LINX (11%). After diaphragmatic re-approximation, DI decreased by a median 0.77 mm2/mm Hg [95%-confidence interval (CI): −0.99, −0.58; P < 0.0001], CSA decreased 16.0 mm2 (95%-CI: −20.0, −8.0; P < 0.0001), whereas HPZ length increased 0.5 cm (95%-CI: 0.5, 1.0; P < 0.0001). After sphincter augmentation, DI decreased 0.14 mm2/mm Hg (95%-CI: −0.30, −0.04; P = 0.0005) and CSA decreased 5.0 mm2 (95%-CI: −10.0, 1.0; P = 0.0.0015), whereas HPZ length increased 0.5 cm (95%-CI: 0.50, 0.54; P < 0.0001). Diaphragmatic re-approximation had a higher percent contribution to distensibility (79% vs 21%), CSA (82% vs 18%), and HPZ (60% vs 40%) than sphincter augmentation. Conclusion: Dynamic intraoperative monitoring demonstrates that diaphragmatic re-approximation and sub-diaphragmatic relocation has a greater effect on EGJ compliance than sphincter augmentation. As such, antireflux procedures should address both for optimal improvement of EGJ physiology.
Left handedness and response to repetitive transcranial magnetic stimulation in major depressive disorder

Abstract Objectives Considerable research has demonstrated the efficacy of repetitive transcranial magnetic stimulation treatment (rTMS) in patients with major depressive disorder (MDD) with differences in effects related to laterality of stimulation. However, no systematic research has explored whether left-handed subjects respond in the same way as right-handed subjects. Methods Data from 6 clinical trials (n = 310) were pooled and we explored whether left-handed patients with MDD responded in a similar manner to rTMS, including how they responded to both high-frequency left and low-frequency right-sided forms of treatment. Results Overall, patients with MDD who were left-handed responded to a greater degree than right-handed patients to rTMS therapy. On subgroup analysis, notably limited by small numbers in the left handed groups, this effect was seen with high-frequency left-sided treatment but not with low-frequency right-sided treatment. The overall effect of a greater response in left-handed patients was not attributable to other clinical or study variables. Conclusions Standard forms of rTMS treatment appear to be effective in patients with MDD who are left-handed and there seems no justification for modifying the laterality of treatment application in these patients.
Examining the Role of Childhood Adversity on Excess Alcohol Intake and Tobacco Exposure among US College Students

Abstract Background Adverse childhood experiences (ACEs) are often associated with substance use behaviors such as drinking excess alcohol and tobacco use. Resilience may protect individuals from engaging in these maladaptive behaviors following ACEs. Objectives: We examined the associations between ACEs and excessive alcohol consumption, and ACEs and tobacco intake and exposure among diverse college students, and whether resilience buffered this relationship. Methods: We conducted a cross-sectional online survey in October 2018 with students at a large Southern university to assess ACEs, levels of resilience, and students’ health behaviors. We used the Adverse Childhood Experiences – International Questionnaire (ACE-IQ) and the Brief Resilience Scale. Logistic regression modeled the relationship between ACEs and students’ substance use behaviors. We adjusted for demographics, other health behaviors, and emotional health and we tested resilience as a possible buffer. Results: Participants (n = 568) were in their early twenties, almost three-fourths were female. We had a racially/ethnically diverse sample. Over two-thirds had experienced 1–4 ACEs. ACE exposure was not associated with excess alcohol consumption but exhibited a consistent dose-response relationship in unadjusted and adjusted models. Moderate ACEs increased the odds of tobacco exposure by 227% (OR: 3.27, 95% CI: 1.17–9.11) in adjusted models. Resilience was unrelated to either behavior. Black respondents had significantly reduced odds for both substance use outcomes. Tobacco exposure and excess alcohol intake were comorbid behaviors. Conclusion: Childhood adversity was a significant predictor for tobacco exposure among diverse US college students. Resilience did not buffer this relationship. Age, gender, and race/ethnicity were differentially associated with substance use.
Mitochondrial bioenergetics, glial reactivity and pain-related behavior can be restored by dichloroacetate treatment in rodent pain models.

Glial reactivity in the dorsal horn of the spinal cord is a hallmark in most chronic pain conditions. Neuroinflammation-associated reactive glia, in particular astrocytes, have been shown to exhibit reduced mitochondrial respiratory function.Here we studied the mitochondrial function at the lumbar spinal cord tissue from Complete Freund's adjuvant (CFA)-induced inflammatory pain rat and chronic constriction injury (CCI) mouse models by high resolution respirometry (HRR). A significant decrease in mitochondrial bioenergetic parameters at the injury-related spinal cord level coincided with highest astrocytosis. Oral administration of dichloroacetate (DCA) significantly increased mitochondrial respiratory function by inhibiting pyruvate dehydrogenase kinase (PDK) and decreased GFAP and Iba-1 immunoreactivity in spinal cord. Importantly, DCA treatment significantly reduced the ipsilateral pain-related behavior without affecting contralateral sensitivity in both pain models. Our results indicate that mitochondrial metabolic modulation with DCA may offer an alternative therapeutic strategy to alleviate chronic and persistent inflammatory pain.
Coagulation Abnormalities and Thrombosis in Patients Infected With SARS-CoV-2 and Other Pandemic Viruses

The world is amid a pandemic caused by severe acute respiratory syndrome-coronavirus 2. Severe acute respiratory syndrome-coronavirus causes serious respiratory tract infections that can lead to viral pneumonia, acute respiratory distress syndrome, and death. Some patients with coronavirus disease 2019 (COVID-19) have an activated coagulation system characterized by elevated plasma levels of d-dimer—a biomarker of fibrin degradation. Importantly, high levels of D-dimer on hospital admission are associated with increased risk of mortality. Venous thromboembolism is more common than arterial thromboembolism in hospitalized COVID-19 patients. Pulmonary thrombosis and microvascular thrombosis are observed in autopsy studies, and this may contribute to the severe hypoxia observed in COVID-19 patients. It is likely that multiple systems contribute to thrombosis in COVID-19 patients, such as activation of coagulation, platelet activation, hypofibrinolysis, endothelial cell dysfunction, inflammation, neutrophil extracellular traps, and complement. Targeting these different pathways may reduce thrombosis and improve lung function in COVID-19 patients.
An optimality‐based model explains seasonal variation in C3 plant photosynthetic capacity

The maximum rate of carboxylation (Vcmax) is an essential leaf trait determining the photosynthetic capacity of plants. Existing approaches for estimating Vcmax at large scale mainly rely on empirical relationships with proxies such as leaf nitrogen/chlorophyll content or hyperspectral reflectance, or on complicated inverse models from gross primary production or solar‐induced fluorescence. A novel mechanistic approach based on the assumption that plants optimize resource investment coordinating with environment and growth has been shown to accurately predict C3 plant Vcmax based on mean growing season environmental conditions. However, the ability of optimality theory to explain seasonal variation in Vcmax has not been fully investigated. Here, we adapt an optimality‐based model to simulate daily Vcmax,25C (Vcmax at a standardized temperature of 25°C) by incorporating the effects of antecedent environment, which affects current plant functioning, and dynamic light absorption, which coordinates with plant functioning. We then use seasonal Vcmax,25C field measurements from 10 sites across diverse ecosystems to evaluate model performance. Overall, the model explains about 83% of the seasonal variation in C3 plant Vcmax,25C across the 10 sites, with a medium root mean square error of 12.3 μmol m−2 s−1, which suggests that seasonal changes in Vcmax,25C are consistent with optimal plant function. We show that failing to account for acclimation to antecedent environment or coordination with dynamic light absorption dramatically decreases estimation accuracy. Our results show that optimality‐based approach can accurately reproduce seasonal variation in canopy photosynthetic potential, and suggest that incorporating such theory into next‐generation trait‐based terrestrial biosphere models would improve predictions of global photosynthesis.
Polymorphisms in BMPR-IB gene and their association with litter size trait in Chinese Hu sheep

Abstract Identification and utilization of sheep major fecundity genes offer opportunities for the increase in litter size, as well as the improvement of production efficiency in livestock industry. BMPR-IB gene belongs to the TGF-β superfamily, and is also considered as a regulator for sheep reproductive performance due to its involvement in the mammalian gametogenesis pathway. This study aimed to detect the variations of BMPR-IB gene in Hu sheep (N = 934) and to evaluate their effects on the litter size trait. qRT-PCR results showed that the mRNA expression level of BMPR-IB in kidney was the highest. And in the tissues of ovary and pituitary, the expression levels of prolific group were significantly higher than that of non-prolific group (p < 0.05). Through DNA sequencing and PCR-RFLP, three SNPs were identified in the genomic region of BMPR-IB gene; the individuals with CC in g.29362047T > C, AA in g.29427689G > A and GG in FecB had better fecundity characterization. Additionally, association analysis indicated that two diplotypes of Hap2/2 and Hap2/4 showed larger litter size. Overall, our results verified several useful markers which would contribute to further development of sheep breeding strategies.
Can chilling tolerance of C4 photosynthesis in Miscanthus be transferred to sugarcane?

The goal of this study was to investigate whether chilling tolerance of C4 photosynthesis in Miscanthus can be transferred to sugarcane by hybridization. Net leaf CO2 uptake (Asat) and the maximum operating efficiency of photosystem II (ФPSII) were measured in warm conditions (25 °C/20 °C), and then during and following a chilling treatment of 10 °C/5 °C for 11 day in controlled environment chambers. Two of three hybrids (miscanes), ‘US 84‐1058’ and ‘US 87‐1019’, did not differ significantly from the chilling tolerant M. ×giganteus ‘Illinois’ (Mxg), for Asat, and ΦPSII measured during chilling. For Mxg grown at 10 °C/5 °C for 11 days, Asat was 4.4 μmol m−2 s−1, while for miscane ‘US 84‐1058’ and ‘US 87‐1019’, Asat was 5.7 and 3.5 μmol m−2 s−1, respectively. Miscanes ‘US 84‐1058’ and ‘US 87‐1019’ and Mxg had significantly higher rates of Asat during chilling than three tested sugarcanes. A third miscane showed lower rates than Mxg during chilling, but recovered to higher rates than sugarcane upon return to warm conditions. Chilling tolerance of ‘US 84‐1058’ was further confirmed under autumn field conditions in southern Illinois. The selected chilling tolerant miscanes have particular value for biomass feedstock and biofuel production and at the same time they can be a starting point for extending sugarcane's range to colder climates.
Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding

Abstract Nuclear proteins bind chromatin to execute and regulate genome-templated processes. While studies of individual nucleosome interactions have suggested that an acidic patch on the nucleosome disk may be a common site for recruitment to chromatin, the pervasiveness of acidic patch binding and whether other nucleosome binding hot-spots exist remain unclear. Here, we use nucleosome affinity proteomics with a library of nucleosomes that disrupts all exposed histone surfaces to comprehensively assess how proteins recognize nucleosomes. We find that the acidic patch and two adjacent surfaces are the primary hot-spots for nucleosome disk interactions, whereas nearly half of the nucleosome disk participates only minimally in protein binding. Our screen defines nucleosome surface requirements of nearly 300 nucleosome interacting proteins implicated in diverse nuclear processes including transcription, DNA damage repair, cell cycle regulation and nuclear architecture. Building from our screen, we demonstrate that the Anaphase-Promoting Complex/Cyclosome directly engages the acidic patch, and we elucidate a redundant mechanism of acidic patch binding by nuclear pore protein ELYS. Overall, our interactome screen illuminates a highly competitive nucleosome binding hub and establishes universal principles of nucleosome recognition.