Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring consequences of simulation design for apparent performance of methods of meta-analysis

Contemporary statistical publications rely on simulation to evaluate performance of new methods and compare them with established methods. In the context of random-effects meta-analysis of log-odds-ratios, we investigate how choices in generating data affect such conclusions. The choices we study include the overall log-odds-ratio, the distribution of probabilities in the control arm, and the distribution of study-level sample sizes. We retain the customary normal distribution of study-level effects. To examine the impact of the components of simulations, we assess the performance of the best available inverse–variance–weighted two-stage method, a two-stage method with constant sample-size-based weights, and two generalized linear mixed models. The results show no important differences between fixed and random sample sizes. In contrast, we found differences among data-generation models in estimation of heterogeneity variance and overall log-odds-ratio. This sensitivity to design poses challenges for use of simulation in choosing methods of meta-analysis.
RUBIC (ReproUnion Biobank and Infertility Cohort): A binational clinical foundation to study risk factors, life course, and treatment of infertility and infertility‐related morbidity

Infertility affects 15%–25% of all couples during their reproductive life span. It is a significant societal and public health problem with potential psychological, social, and economic consequences. Furthermore, infertility has been linked to adverse long‐term health outcomes. Despite the advanced diagnostic and therapeutic techniques available, approximately 30% of infertile couples do not obtain a live birth after fertility treatment. For these couples, there are no further options to increase their chances of a successful pregnancy and live birth.
Effects of plant growth promoting Rhizobacteria microbial on the growth, rhizosphere soil properties, and bacterial community of Pinus sylvestris var. mongolica seedlings

ABSTRACT The use of plant growth promoting rhizobacteria (PGPR) instead of pesticides to promote plant growth has received widespread attention. In this study, potted experiments and high-throughput Illumina MiSeq sequencing technology were used to evaluate the effects of inoculation of three PGPR strains on the biomass of Pinus sylvestris var. mongolica and soil bacterial diversity. The results showed that the three PGPR strains all have the ability to secrete indole-3-acetic acid (IAA), dissolve inorganic phosphorus and produce siderophores. After inoculation with the PGPR strain, the plant seedling height increased significantly by 27.60%, and the root length increased significantly by 47.88% (P < 0.05), soil available nitrogen, phosphorus and potassium increased by 19.05%-47.62%, 26.63%-83.32% and 87.70%-98.10% respectively (P < 0.05). High-throughput sequencing results showed that the abundant bacterial phyla in soil include: Acidobacteria, Patescibacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Firmicutes, Actinobacteria, and Proteobacteria. The Monte-Carlo permutation test indicated that soil AP, TP, AK, and OM were the main environmental parameters influencing the composition of the microbial communities (at the genus level). This study provides basic data references for PGPR strains to improve the soil microecological environment and promote the growth and development of Pinus sylvestris var. mongolica seedlings.
PHARMACOKINETICS OF A SINGLE ORAL DOSE OF PONAZURIL IN THE INDIAN PEAFOWL (PAVO CRISTATUS)

Abstract: Ponazuril, a novel coccidiocidal triazinetrione, has shown promise in addressing apicomplexan diseases in mammals and birds. This study describes the pharmacokinetics of ponazuril in healthy adult Indian peafowl (Pavo cristatus) following a single oral dose administered at two different dosages. Peafowl (four males and four females) were administered compounded ponazuril at 20 or 40 mg/kg orally in a double crossover design, with a 2-wk washout period. Blood was collected from each bird at 2, 4, 8, 24, 48, 72, 96, and 120 h after administration for plasma concentration of ponazuril using high-pressure liquid chromatography. Fecals were evaluated for coccidial shedding for 3 consecutive d prior to the ponazuril trial, 1 wk after the first dose of ponazuril, and 1 wk after the second dose of the trial. After the first trial, one peafowl administered 20 mg/kg ponazuril was shedding coccidia, but no coccidia were detected by the end of the second trial. Ponazuril reached peak concentrations (Tmax) at 21.38 h + 5.25 and 22.04 h + 7.39, and peak concentration (Cmax) were 11.82 µg/ml + 3.01 and 18.42 µg/ml + 4.13, for 20 and 40 mg/kg doses, respectively. Ponazuril was detected at 120 h with a concentration of 9.48 µg/ml + 2.59 and 12.25 µg/ml + 2.89 and a half-life of 219.4 + 58.7 h and 186.7 + 58.7 h, for and 40 mg/kg doses, respectively. Ponazuril in peafowl was well absorbed orally, plasma concentrations increased with dose, and elimination was slower than current dosages for birds would suggest. No obvious adverse effects were observed at either dosage.
TERBINAFINE PHARMACOKINETICS FOLLOWING SINGLE-DOSE ORAL ADMINISTRATION IN RED-EARED SLIDER TURTLES (TRACHEMYS SCRIPTA ELEGANS): A PILOT STUDY

Abstract: In this pilot study, the pharmacokinetics of terbinafine were determined in six apparently healthy red-eared slider turtles (Trachemys scripta elegans) after a single PO administration. Terbinafine suspension (15 mg/kg, once) was administered via gavage tube to all turtles. Blood samples were collected immediately before (time 0) and at 1, 2, 4, 8, 24, and 48 h after drug administration. Plasma terbinafine concentrations were quantified by ultra-performance liquid chromatography–mass spectrometry, and noncompartmental pharmacokinetic analysis was performed. None of the animals showed any adverse responses following terbinafine administration. Mean area under the curve from time 0 to 24 h was 1,213 h × ng/ml (range 319–7,309), mean peak plasma concentration was 201.5 ng/ml (range 45.8–585.3), mean time to maximum plasma concentration was 1.26 h (range 1–4), mean residence time was 7.71 h (range 3.85–14.8), and mean terminal half-life was 5.35 h (range 2.67–9.83). The administration of terbinafine (15 mg/kg, PO) may be appropriate for treatment of select fungal organisms with low minimum inhibitory concentrations in red-eared slider turtles but may require q12h administration even for organisms with low minimum inhibitory concentrations. Multiple-dose studies as well as clinical studies are needed to determine ideal dosages and efficacy.
A RETROSPECTIVE STUDY OF NEOPLASIA IN NONDOMESTIC FELIDS IN HUMAN CARE, WITH A COMPARATIVE LITERATURE REVIEW

Abstract: This retrospective study of neoplasia in nondomestic felids in human care presents the cases diagnosed at Northwest ZooPath (NWZP), Monroe, Washington, from 1998 to 2017 in conjunction with a scoping literature review. The 554 neoplasms identified in 20 species in the NWZP archive were combined with the 984 neoplasms identified in those same species in the published literature. Some of the cases identified in the literature were from the NWZP archive. Based on this review, mammary adenocarcinoma (183/1,483, 12.3%), lymphoma (89/1,483, 6.0%), squamous cell carcinoma (85/1,483, 5.7%), pheochromocytoma (57/1,483, 3.8%), and thyroid adenoma (57/1,483, 3.8%) are the most frequently reported neoplasms in nondomestic felids in human care. Apparent species predilections for neoplasia include mammary adenocarcinoma in tigers, jaguars, lions, and jungle cats; lymphoma in lions and tigers; squamous cell carcinoma in snow leopards; pheochromocytoma in clouded leopards; ovarian adenocarcinoma in jaguars; cholangiocarcinoma in lions and tigers; multiple myeloma in tigers; bronchoalveolar adenocarcinoma in cougars and lions; hemangiosarcoma, hepatocellular carcinoma, and gastrointestinal adenocarcinoma in lions; mesothelioma in clouded leopards, lions, and tigers; myelolipoma and cutaneous mast cell tumor in cheetahs; soft tissue sarcomas in tigers; and transitional cell carcinoma of the urinary bladder in fishing cats.
ECHOCARDIOGRAPHY AND DIRECT ARTERIAL BLOOD PRESSURE MEASUREMENT IN CAPTIVE CHIMPANZEES (PAN TROGLODYTES) DURING TWO PHASES OF AN ANESTHETIC PROTOCOL

Abstract: The effects of α-2 agonists on echocardiographic findings in great apes are not well documented, and knowledge of these effects would expand the understanding of cardiac examinations of chimpanzees under anesthesia with protocols using these drugs. Ten adult chimpanzees (Pan troglodytes), four males and six females, underwent echocardiographic examinations after anesthesia with dexmedetomidine, midazolam, and ketamine (phase 1). Four animals required isoflurane to achieve an adequate plane of anesthesia. Atipamezole was used to antagonize dexmedetomidine, and all remaining animals were placed on isoflurane (phase 2), and then a second echocardiogram was performed. Direct arterial blood pressure was monitored during the anesthetic event. Measurements and recordings were assessed for statistically significant differences between the two phases and sex. There were no significant differences between phases or sex for any two-dimensional echocardiographic measurement of systolic function, although interventricular septum thickness at end systole approached a significant decrease from phase 1 to phase 2 (P = 0.058) when sex was considered a between-subject factor. Left ventricular outflow tract (P = 0.017) and pulmonary artery (P = 0.028) velocities increased after reversal of the dexmedetomidine. Diastolic transmitral flow was consistent with grade 3 diastolic dysfunction (median early to late ventricular filling velocities (E/A) of 2.02, interquartile range [IQR], 1.53–2.13) with a nonsignificant decrease of E velocity and increase in A velocity and decreased E/A after reversal. Trace mitral and tricuspid regurgitation were common findings in the sample population. Arterial blood pressure significantly decreased between phase 1 and phase 2 (P < 0.01). All chimpanzees entered a hypotensive state (mean arterial pressure < 60 mm Hg) during phase 2. Although limited by the small number of chimpanzees, this study showed an increase in afterload, potential diastolic dysfunction, and a decrease in blood pressure after the antagonism of dexmedetomidine. Additional studies to further assess the effects of α-2 agonists in chimpanzees are warranted.
A RETROSPECTIVE REVIEW OF THE CLINICAL UTILITY OF FECAL BACTERIAL ENTERIC PATHOGEN CULTURES IN MAMMALS WITHIN A ZOOLOGICAL COLLECTION AND THE USE OF FECAL CYTOLOGY FOR OPTIMIZATION OF DIAGNOSTIC TESTING

Abstract: To determine the diagnostic value of fecal bacterial enteric pathogen cultures (FBEPC) as part of routine preventive medicine protocols in terrestrial mammals housed in a zoological collection, this study investigated the clinical utility of FBEPC results in context of subsequent clinical actions and how its use was rationalized after adjunct use of fecal cytology as a first-line diagnostic tool. Retrospective results (n = 692) that included a routine FBEPC panel of a commercial diagnostic laboratory, including Aeromonas, Salmonella, Campylobacter, Plesiomonas, Shigella, Yersinia, and Edwardsiella, of 417 mammals were organized into preventive (P; n = 485), diagnostic (D; n = 177), or recheck (R; n = 30) samples; for P and D samples, findings were assigned a “clinical significance factor” of 1 to 5 according to culture results and subsequent clinical actions. A score of 3 or higher indicated positive growth of potentially pathogenic bacterial organisms, of which there were 50 FBEPC (P n = 27, D n = 20, R n = 3). The difference in mean clinical significance factor for P versus D samples was significant. Aeromonas spp. were most frequently isolated (n = 32), followed by Salmonella spp. (n = 8) and Plesiomonas shigelloides (n = 8), then Campylobacter spp. (n = 5). There was no growth of Yersinia enterocolitica, Shigella spp. , or Edwardsiella spp. In the absence of clinical evidence of gastrointestinal disease, treatment was initiated in only two cases with isolated Campylobacter spp. Implementation of fecal cytology as an initial step in fecal evaluation resulted in a prompt, substantial reduction in number of ordered FBEPC (mean n = 12/month before and n = 5/month after implementation). The findings in this study suggest that FBEPC for these bacterial species has limited value as a screening tool in preventive medicine protocols for the mammalian orders best represented in this study. The use of fecal cytology led to a more targeted and cost-effective use of FBEPC. Fecal cytology as an initial step in preventative and diagnostic testing protocols is recommended.
Language ecology, language endangerment, and relict languages: Case studies from Adamawa (Cameroon-Nigeria)

Abstract As a contribution to the more general discussion on causes of language endangerment and death, we describe the language ecologies of four related languages (Bà Mambila [mzk]/[mcu], Sombә (Somyev or Kila) [kgt], Oumyari Wawa [www], Njanga (Kwanja) [knp]) of the Cameroon-Nigeria borderland to reach an understanding of the factors and circumstances that have brought two of these languages, Sombә and Njanga, to the brink of extinction; a third, Oumyari, is unstable/eroded, while Bà Mambila is stable. Other related languages of the area, also endangered and in one case extinct, fit into our discussion, though with less focus. We argue that an understanding of the language ecology of a region (or of a given language) leads to an understanding of the vitality of a language. Language ecology seen as a multilayered phenomenon can help explain why the four languages of our case studies have different degrees of vitality. This has implications for how language change is conceptualised: we see multilingualism and change (sometimes including extinction) as normative.
Numerical investigation of magnetohydrodynamics Williamson nanofluid flow over an exponentially stretching surface

This research work describes the investigation of a magnetohydrodynamic flow of Williamson nanofluid over an exponentially porous stretching surface considering two cases of heat transfer i.e., prescribed exponential order surface temperature (PEST), and prescribed exponential order heat flux (PEHF). As a result of this infestation, a mathematical model of the problem based on conservation of linear momentum and law of conservation of mass and energy is developed. Whereas governing nonlinear partial differential equations (PDEs) are converted to nonlinear ordinary differential equations (ODEs). Subsequently, the velocity, concentration, and temperature profiles are developed by using the method of similarity transformation. Furthermore, the effects of various physical parameters of engineering interests are demonstrated graphically. It is highlighted that both the magnetic parameter ( M ) and Williamson parameter ( λ ) causes to reduce the boundary layer thickness.
Intermodal Priming of Cognitive Conflict? A Failed Replication of Mager et al. (2009)

Introduction: The present study was conducted to verify a promising experimental setup which demonstrated an inversed Stroop-effect (much faster responses for incongruent relative to congruent Stroop trials) following a mismatching tone. In the matching condition, which was an almost exact replication of the original study, participants were required to indicate whether word color and word meaning were matching, whereas in the response conflict condition, instruction was the same as in a classical Stroop task and required the participants to respond to the word color. As in the original study, each trial was preceded by a sine tone which was deviant in pitch in 20% of the trials. Results: The main result was that the Stroop effect was not inversed after deviant tones, neither under the matching task instruction nor under the response conflict task instruction. The Stroop effect was unaffected by the previous “conceptual mismatch. ” Conclusion: The current study failed to replicate the astonishing concept of “conflict priming” reported in previous work and does not open the doors for a new window on sequences of conflicts. Nevertheless, the failed replication is valuable for future research, since it demonstrated that “Conflict Priming” as a facilitation of processing of conflict trials following deviant tones, is not an confirmed finding.
Protective Effect of Chlorogenic Acid and Its Analogues on Lead-Induced Developmental Neurotoxicity Through Modulating Oxidative Stress and Autophagy

Lead (Pb) is among the deleterious heavy metal and has caused global health concerns due to its tendency to cause a detrimental effect on the development of the central nervous system (CNS). Despite being a serious health concern, treatment of Pb poisoning is not yet available, reflecting the pressing need for compounds that can relieve Pb-induced toxicity, especially neurotoxicity. In the quest of exploring protective strategies against Pb-induced developmental neurotoxicity, compounds from natural resources have gained increased attention. Chlorogenic acid (CGA) and its analogues neochlorogenic acid (NCGA) and cryptochlorogenic acid (CCGA) are the important phenolic compounds widely distributed in plants. Herein, utilizing zebrafish as a model organism, we modeled Pb-induced developmental neurotoxicity and investigated the protective effect of CGA, NCGA, and CCGA co-treatment. In zebrafish, Pb exposure (1,000 μg/L) for 5 days causes developmental malformation, loss of dopaminergic (DA) neurons, and brain vasculature, as well as disrupted neuron differentiation in the CNS. Additionally, Pb-treated zebrafish exhibited abnormal locomotion. Notably, co-treatment with CGA (100 µM), NCGA (100 µM), and CCGA (50 µM) alleviated these developmental malformation and neurotoxicity induced by Pb. Further underlying mechanism investigation revealed that these dietary phenolic acid compounds may ameliorate Pb-induced oxidative stress and autophagy in zebrafish, therefore protecting against Pb-induced developmental neurotoxicity. In general, our study indicates that CGA, NCGA, and CCGA could be promising agents for treating neurotoxicity induced by Pb, and CCGA shows the strongest detoxifying activity.
Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation. ABSTRACT Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural, or industrial settings, the organisms must be profiled at the species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760-nucleotide (nt) region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a 16-member Pseudomonas species mock community. All 16 species were correctly and semiquantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3-V4 amplicon sequencing only correctly identified one species. We analyzed the Pseudomonas profiles in 13 soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the 16S rRNA gene abundance, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and 10 from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD amplicon approach identified more species than were found by cultivation, including hard-to-culture nonfluorescent pseudomonads, as well as more than were found by 16S rRNA V3-V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large-scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method. IMPORTANCE A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.
It happened again: Convergent evolution of acylglucose specialized metabolism in black nightshade and wild tomato

Plants synthesize myriad phylogenetically-restricted specialized (aka ‘secondary’) metabolites with diverse structures. Metabolism of acylated sugar esters in epidermal glandular secreting trichomes across the Solanaceae (nightshade) family are ideal for investigating the mechanisms of evolutionary metabolic diversification. We developed methods to structurally analyze acylhexose mixtures by 2D NMR, which led to the insight that the Old World species black nightshade (Solanum nigrum) accumulates acylglucoses and acylinositols in the same tissue. Detailed in vitro biochemistry – cross validated by in vivo virus induced gene silencing – revealed two unique features of the four-step acylglucose biosynthetic pathway: a trichome-expressed, neofunctionalized invertase-like enzyme, SnASFF1, converts BAHD-produced acylsucroses to acylglucoses, which in turn are substrates for the first-reported acylglucose acyltransferase, SnAGAT1. This biosynthetic pathway evolved independently from that recently described in the wild tomato S. pennellii, reinforcing that acylsugar biosynthesis is evolutionarily dynamic with independent examples of primary metabolic enzyme cooption and additional variation in BAHD acyltransferases. Teaser Analysis of plant protective surface hair chemistry revealed evolutionary mechanisms leading to metabolic innovation.
Pulsation changes link to impaired glymphatic function in a mouse model of vascular cognitive impairment

Large vessel disease and carotid stenosis are key mechanisms contributing to vascular cognitive impairment (VCI) and dementia. Our previous work, and that of others, using rodent models, demonstrated that bilateral common carotid stenosis (BCAS) leads to cognitive impairment via gradual deterioration of the glial-vascular unit and accumulation of amyloid-β (Aβ) protein. Since brain-wide drainage pathways (glymphatic) for waste clearance, including Aβ removal, have been implicated in the pathophysiology of VCI via glial mechanisms, we hypothesized that glymphatic function would be impaired in a BCAS model and exacerbated in the presence of Aβ. Male wild- type and Tg-SwDI (model of microvascular amyloid) mice were subjected to BCAS or sham surgery which led to a reduction in cerebral perfusion and impaired spatial learning and memory. After 3 months survival, glymphatic function was evaluated by cerebrospinal fluid (CSF) fluorescent tracer influx. We demonstrated that BCAS caused a marked regional reduction of CSF tracer influx in the dorsolateral cortex and CA1-DG molecular layer. In parallel to these changes increased reactive astrogliosis was observed post-BCAS. To further investigate the mechanisms that may lead to these changes, we measured the pulsation of cortical vessels. BCAS impaired vascular pulsation in pial arteries in WT and Tg-SwDI mice. Since our findings show that BCAS may influence VCI by impaired glymphatic drainage and reduced vascular pulsation we propose that these additional targets need to be considered when treating VCI.