Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy and Animal Welfare Impacts of Novel Capture Methods for Two Species of Invasive Wild Mammals in New Zealand

Simple Summary The animal welfare impacts of wildlife capture methods are an important contemporary issue in conservation. We assessed novel methods for capturing Bennett’s wallabies (Notamacropus rufogriseus) and red deer (Cervus elaphus), both invasive mammals in New Zealand. The methods assessed were helicopter net-gunning for both species, versus ground-based netting for wallabies and helicopter darting for deer. We quantified efficacy, duration of procedures, frequency of adverse events, and cost-effectiveness for each method. We discuss the benefits of our approach for assessing new wildlife capture methods. Abstract All capture methods impose animal welfare impacts, but these impacts are rarely quantified or reported. We present data from two wildlife capture studies that trialled new methods for capturing Bennett’s wallabies (Notamacropus rufogriseus) and red deer (Cervus elaphus) in New Zealand. We used helicopter net-gunning for both species, and compared this method with ground-based netting for wallabies and helicopter darting for red deer, using, for the first time in New Zealand, the fast-acting opioid thiafentanil. Efficacy and animal welfare parameters quantified were duration of handling and recovery, and frequency of adverse events, including escape, injury, and mortality. Cost-effectiveness was quantified for each method. Capture mortalities occurred for all methods for both species. For red deer, chemical immobilisation led to fewer traumatic injuries and fewer mortalities, while for wallabies, net-gunning led to fewer mortalities. Net-gunning was an efficient capture method for deer in open habitat, but led to the escape of 54% of wallabies and one wallaby mortality (4%). Ground-based netting resulted in the mortality of 17% of wallabies at the time of capture, and the capture of non-target species. The cost per captured wallaby was 40% more expensive for net-gunning (NZ$1045) than for ground-based netting (NZ$745), but, once corrected for mortalities at the time of capture and suitability of individuals for GPS-collar deployment, this was reduced to 29% and 12% more expensive, respectively. Net-gunning for red deer resulted in the escape of 13% of animals and mortality of 10% of animals at the time of capture. Helicopter-based darting for red deer using thiafentanil (c. 0.03–0.06 mg/kg) had high capture efficacy (zero escapes), rapid induction times (mean of 3 min), and a low mortality rate at 14 days post-capture (3%), but it was more expensive per deer captured and collared than aerial netting (NZ$2677 and NZ$2234, respectively). We recommend reporting of adverse event data for all wildlife capture techniques to permit continual refinement of field methods.
Anti‐SOX1 antibody‐positive paraneoplastic neurological syndrome presenting with Lambert‐Eaton myasthenic syndrome and small cell lung cancer: A case report

Paraneoplastic neurological syndromes (PNS) are rare disorders affecting any part of the central, peripheral or autonomic nervous system that occur in association with cancer. Among cancer patients, less than 1% overall develop PNS. Anti‐SOX1 antibodies' positive paraneoplastic neurological disorders are rare and are usually associated with small cell lung cancer (SCLC). Here, we report a case of a 61‐year‐old male patient who presented with an unusual anti‐SOX1 positive PNS. The right tibialis anterior showed noticeable low‐amplitude motor unit potentials and high amplitude motor potentials in electrodiagnostic study, suggesting the presence of Lambert‐Eaton myasthenic syndrome (LEMS). Typical MRI and PET‐CT found a hyperintense lesion with contrast enhancement in the thorax in front of 5–6 centrum of vertebrae, and thoracoscopic biopsy revealed pathological findings for SCLC. The patient underwent several lines of chemotherapy and radiotherapy and survived for 15 months after the diagnosis of SCLC.
Association of Tim-4 expression in monocyte subtypes with clinical course and prognosis in acute ischemic stroke patients

Abstract Background: It has been proven that T cell immunoglobin and mucin domain (Tim)-4 and monocytes (Mo) are involved in regulation of immunity, which is important for the recovery of acute ischemic stroke (AIS). Methods: In this study, the expression of Tim-4 in both circulating Mo subtypes and plasma in 32 consecutive AIS patients and 32 control patients was assessed to determine their correlation with the clinical course and prognosis of AIS. Results: It was found that, compared to the control patients, the percentage of Tim-4 expression in overall Mo, classical Mo and non-classical Mo was significantly elevated after 2 and 5 days of stroke (p < 0.05), while it was promoted from 0 to 10 days of stoke in intermediate Mo (p < 0.05). Furthermore, Tim-4 expressions in non-classical Mo and intermediate Mo were obviously correlated with National Institutes of Health Stroke Scale (NIHSS) scores at 2 days of stroke (r = 0.351, p = 0.048; r = 0.358, p = 0.044, respectively). In poor outcome (PO) patients, the expression of Tim-4 in non-classical Mo was remarkably promoted at 2 days of stroke in comparison with non-PO patients (p < 0.05). More importantly, our results revealed a positive correlation between Tim-4 expression in non-classical Mo and interleukin (IL)-6 plasma levels in AIS patients without infection. Conclusion: In summary, our findings proved that Tim-4 expression in non-classical Mo could be an appropriate target for the prediction of the clinical course and prognosis in AIS patients.
Cancer Risk following Radioactive Iodine Treatment for Hyperthyroidism: a Cohort Study.

BACKGROUND Radioactive iodine is in widespread use for the treatment of hyperthyroidism. Data on long-term safety outcome are limited and conflicting. The objectives of this study were to evaluate the association of radioiodine treatment for hyperthyroidism with overall cancer and with specific cancer types. METHODS This is a historical cohort study, using the Clalit healthcare database. Participants were all adults with a new diagnosis of hyperthyroidism in 2002 to 2015, newly treated with radioactive iodine, or with thionamides (propylthiouracil/thiamazole), excluding patients with previous malignancies. Age, sex, smoking history, body mass index, Clalit district, socioeconomic status, history of diabetes mellitus and of hypertension, use of aspirin and of statins, and adherence to cancer screening procedures were used to calculate propensity-score to receive radioiodine. Incidence rates and 95% confidence intervals were calculated for overall cancer occurrence, and for each cancer type using Poisson distribution. Association between study variables and time to cancer event was evaluated using cause-specific hazard ratios (HR) and 95% confidence intervals (CI), estimated by univariate and propensity-score adjusted multivariable Cox proportional hazards models. For sensitivity analysis we stratified the cohort by calendar year at cohort entry and by length of follow-up. RESULTS 16,637 patients formed the study cohort, with 123,166 person-years of follow-up. There was no association between radioiodine treatment and increased risk of overall cancer HR=0.99 (0.83-1.19, p=0.91), HR= 1.01 (0.83-1.21, p=0.95) (univariate and multivariable analyses, respectively). However, in a sensitivity analysis, we found an association with overall cancer risk in the first period of follow-up (up to 4.2 years) HR 2.11 (1.59-2.80) (p<0.0001), and no association with increased risk in a longer follow-up period. An association was found between radioiodine exposure and an increased risk for non-Hodgkin's lymphoma (NHL), in univariate but a non-significant increased risk in multivariable analysis: HR 2.89 (1.12-7.46,p=0.03), HR 2.32 (0.88-6.13,p=0.09), respectively. CONCLUSIONS No association was found between radioiodine treatment for hyperthyroidism and risk for incident cancer in long-term follow-up. In an analysis of specific cancer types, a statistically significant association was found with NHL only in univariate analysis.
Rescue of tomato spotted wilt virus entirely from complementary DNA clones

Significance Although reverse genetics (RG) systems were first developed for animal-infecting viruses with segmented negative-stranded/ambisense RNA genomes over 20 years ago, such a system for plant viruses with segmented negative-stranded/ambisense RNA genomes had not been developed until now. Tomato spotted wilt virus (TSWV), a virus with tripartite negative-stranded/ambisense RNA genomes, is one of the most economically important plant viruses in the world. Many groups have tried to construct infectious clones for TSWV, but all have failed. Here we report the establishment of a RG system for TSWV. Infectious TSWV and derivatives carrying eGFP reporters were rescued entirely from complementary DNA (cDNA) clones. This RG system now provides a powerful platform to study the disease pathology of Tospoviruses during natural infection. Negative-stranded/ambisense RNA viruses (NSVs) include not only dangerous pathogens of medical importance but also serious plant pathogens of agronomic importance. Tomato spotted wilt virus (TSWV) is one of the most important plant NSVs, infecting more than 1,000 plant species, and poses major threats to global food security. The segmented negative-stranded/ambisense RNA genomes of TSWV, however, have been a major obstacle to molecular genetic manipulation. In this study, we report the complete recovery of infectious TSWV entirely from complementary DNA (cDNA) clones. First, a replication- and transcription-competent minigenome replication system was established based on 35S-driven constructs of the S(−)-genomic (g) or S(+)-antigenomic (ag) RNA template, flanked by the 5′ hammerhead and 3′ ribozyme sequence of hepatitis delta virus, a nucleocapsid (N) protein gene and codon-optimized viral RNA-dependent RNA polymerase (RdRp) gene. Next, a movement-competent minigenome replication system was developed based on M(−)-gRNA, which was able to complement cell-to-cell and systemic movement of reconstituted ribonucleoprotein complexes (RNPs) of S RNA replicon. Finally, infectious TSWV and derivatives carrying eGFP reporters were rescued in planta via simultaneous expression of full-length cDNA constructs coding for S(+)-agRNA, M(−)-gRNA, and L(+)-agRNA in which the glycoprotein gene sequence of M(−)-gRNA was optimized. Viral rescue occurred with the addition of various RNAi suppressors including P19, HcPro, and γb, but TSWV NSs interfered with the rescue of genomic RNA. This reverse genetics system for TSWV now allows detailed molecular genetic analysis of all aspects of viral infection cycle and pathogenicity.
Consumer Preferences for Traceable Food with Different Functions of Safety Information Attributes: Evidence from a Menu-Based Choice Experiment in China

It is of great value to study consumer demand for safe foods in promoting the development of a safe food market system and the reduction of food safety risks, as well as foodborne diseases in China. This paper takes traceable pork as an example and constructs food safety information attributes with ex ante quality verification and ex post traceability. Interactions between safety information attributes and the consumer’s response to cost-driven price changes were investigated for 345 consumers in Wuxi City, Jiangsu Province, China, using a menu-based choice (MBC) experiment and multivariate probit (MVP) model as analysis tools. The results suggest that food safety information attributes are important to consumers, as the consumers preferred pork quality inspection attributes to pre-incident quality assurance functions. Therefore, it is beneficial to include pork quality inspection attributes in the traceable pork attribute systems during the initial construction of traceable pork markets in China. Attribute price was an important factor that affected consumers’ choice of information attributes. When customization cannot be achieved, a profile composed of elastic pork quality inspection attribute and supply chain–internal traceability attribute would be the most preferred traceable pork product in the market based on the need of building a fully functional traceable food system and reducing food safety risks. In addition, there was a strong substitution relationship between different information attributes, and there was heterogeneity in consumers’ choice of information attributes. Therefore, the government should support manufacturers in producing multi-level safe food to meet diverse consumer demand.
Retrospective analysis of fetal vertebral defects: Associated anomalies, etiologies, and outcome

Our objectives were to describe fetal cases of vertebral defects (VD), assess the diagnostic yield of fetal chromosomal analysis for VD and determine which investigations should be performed when evaluating fetal VD. We performed a retrospective chart review for fetuses with VD seen between 2006 and 2015. Cases were identified from CHU Sainte‐Justine's prenatal clinic visits, postmortem fetal skeletal surveys, and medical records. Cases with neural tube defects were excluded. Sixty‐six fetuses with VD were identified at a mean gestational age of 20 weeks. Forty‐seven (71.2%) had associated antenatal anomalies, most commonly genitourinary, skeletal/limb, and cardiac anomalies. Thirteen mothers (19.7%) had pregestational diabetes (95% CI [10.1%–29.3%]). Fifty‐three cases had chromosomal analysis. Three had abnormal results (5.6%): trisomy 13, trisomy 22, and 9q33.1q34. 11 deletion. Thirty‐four (51.5%) pregnancies were terminated, one led to intrauterine fetal demise and 31 (46.9%) continued to term. Of 27 children who survived the neonatal period, 21 had congenital scoliosis and 3 had spondylocostal dysostosis. Seven had developmental delay. In conclusion, prenatal evaluation of fetuses with VD should include detailed morphological assessment (including fetal echocardiogram), maternal diabetes screening, and chromosomal microarray if non‐isolated. Our findings provide guidance about management and counseling after a diagnosis of fetal VD.
Uncovering the functional residues of Arabidopsis isoprenoid biosynthesis enzyme HDS

Significance The MEP pathway is an essential and evolutionarily conserved metabolic route present in most pathogenic bacteria, plants, and malaria; and hence a target for discovery of agricultural and medical applications, and an engineering template for production of isoprenoids. The essential nature of this pathway and inherent intricacies associated with enzyme activity assays have hampered in vivo structure and functional analyses. Here, we report the suppressor screen leading to identification of 3 functionally conserved amino-acid residues positioned at the active site cavity and cofactor binding domain of the key MEP-pathway enzyme, HDS. The proposed roles of these residues in determining HDS enzyme activity and the MEP-pathway flux offer a platform for rational design of antiinfective drugs and synthetic engineering of isoprenoids. The methylerythritol phosphate (MEP) pathway is responsible for producing isoprenoids, metabolites with essential functions in the bacterial kingdom and plastid-bearing organisms including plants and Apicomplexa. Additionally, the MEP-pathway intermediate methylerythritol cyclodiphosphate (MEcPP) serves as a plastid-to-nucleus retrograde signal. A suppressor screen of the high MEcPP accumulating mutant plant (ceh1) led to the isolation of 3 revertants (designated Rceh1–3) resulting from independent intragenic substitutions of conserved amino acids in the penultimate MEP-pathway enzyme, hydroxymethylbutenyl diphosphate synthase (HDS). The revertants accumulate varying MEcPP levels, lower than that of ceh1, and exhibit partial or full recovery of MEcPP-mediated phenotypes, including stunted growth and induced expression of stress response genes and the corresponding metabolites. Structural modeling of HDS and ligand docking spatially position the substituted residues at the MEcPP binding pocket and cofactor binding domain of the enzyme. Complementation assays confirm the role of these residues in suppressing the ceh1 mutant phenotypes, albeit to different degrees. In vitro enzyme assays of wild type and HDS variants exhibit differential activities and reveal an unanticipated mismatch between enzyme kinetics and the in vivo MEcPP levels in the corresponding Rceh lines. Additional analyses attribute the mismatch, in part, to the abundance of the first and rate-limiting MEP-pathway enzyme, DXS, and further suggest MEcPP as a rheostat for abundance of the upstream enzyme instrumental in fine-tuning of the pathway flux. Collectively, this study identifies critical residues of a key MEP-pathway enzyme, HDS, valuable for synthetic engineering of isoprenoids, and as potential targets for rational design of antiinfective drugs.
Graph Theory-Based Sequence Descriptors as Remote Homology Predictors

Alignment-free (AF) methodologies have increased in popularity in the last decades as alternative tools to alignment-based (AB) algorithms for performing comparative sequence analyses. They have been especially useful to detect remote homologs within the twilight zone of highly diverse gene/protein families and superfamilies. The most popular alignment-free methodologies, as well as their applications to classification problems, have been described in previous reviews. Despite a new set of graph theory-derived sequence/structural descriptors that have been gaining relevance in the detection of remote homology, they have been omitted as AF predictors when the topic is addressed. Here, we first go over the most popular AF approaches used for detecting homology signals within the twilight zone and then bring out the state-of-the-art tools encoding graph theory-derived sequence/structure descriptors and their success for identifying remote homologs. We also highlight the tendency of integrating AF features/measures with the AB ones, either into the same prediction model or by assembling the predictions from different algorithms using voting/weighting strategies, for improving the detection of remote signals. Lastly, we briefly discuss the efforts made to scale up AB and AF features/measures for the comparison of multiple genomes and proteomes. Alongside the achieved experiences in remote homology detection by both the most popular AF tools and other less known ones, we provide our own using the graphical–numerical methodologies, MARCH-INSIDE, TI2BioP, and ProtDCal. We also present a new Python-based tool (SeqDivA) with a friendly graphical user interface (GUI) for delimiting the twilight zone by using several similar criteria.
Comparative cone-beam computed tomography evaluation of temporomandibular joint position and morphology in female patients with skeletal class II malocclusion

Objective This study was performed to evaluate the position and morphology of the temporomandibular joint in female patients with skeletal class II malocclusion and to investigate the association between temporomandibular joint disorders and facial types using cone-beam computed tomography. Methods A lateral cephalogram was taken to determine the skeletal class of each participant. Sixty female patients aged 16 to 28 years were divided into high-angle, low-angle, and control groups. The shape of the condyle–fossa was measured and assessed on cone-beam computed tomography images of the 120 temporomandibular joints. Results Some condylar shape measurements displayed statistically significant differences among the groups. No significant differences were found in the length of the condyle, width of the glenoid fossa, or height of the articular eminence among the three groups. The posterior condylar position was more frequently observed in the low-angle group, whereas the anterior condylar position was more prevalent in the high-angle group. Conclusion The present study revealed differences in the condyle–fossa morphology and position in female patients with skeletal class II malocclusion with different vertical facial types.
Robust detection of event-related potentials in a user-voluntary short-term imagery task

Event-related potentials (ERPs) represent neuronal activity in the brain elicited by external visual or auditory stimulation and are widely used in brain-computer interface (BCI) systems. The ERP responses are elicited a few milliseconds after attending to an oddball stimulus; target and non-target stimuli are repeatedly flashed, and the ERP trials are averaged over time in order to improve their decoding accuracy. To reduce this time-consuming process, previous studies have attempted to evoke stronger ERP responses by changing certain experimental parameters like color, size, or the use of a face image as a target symbol. Since these exogenous potentials can be naturally evoked by merely looking at a target symbol, the BCI system could generate unintended commands while subjects are gazing at one of the symbols in a non-intentional mental state. We approached this problem of unintended command generation by assuming that a greater effort by the user in a short-term imagery task would evoke a discriminative ERP response. Three tasks were defined: passive attention, counting, and pitch-imagery. Users were instructed to passively attend to a target symbol, or to perform a mental tally of the number of target presentations, or to perform the novel task of imagining a high-pitch tone when the target symbol was highlighted. The decoding accuracy were 71.4%, 83.5%, and 89.2% for passive attention, counting, and pitch-imagery, respectively, after the fourth averaging procedure. We found stronger deflections in the N500 component corresponding to the levels of mental effort (passive attention: -1.094 ±0.88 μV, counting: -2.226 ±0.97 μV, and pitch-imagery: -2.883 ±0.74 μV), which highly influenced the decoding accuracy. In addition, the rate of binary classification between passive attention and pitch-imagery tasks was 73.5%, which is an adequate classification rate that motivated us to propose a two-stage classification strategy wherein the target symbols are estimated in the first stage and the passive or active mental state is decoded in the second stage. In this study, we found that the ERP response and the decoding accuracy are highly influenced by the user’s voluntary mental tasks. This could lead to a useful approach in practical ERP systems in two respects. Firstly, the user-voluntary tasks can be easily utilized in many different types of BCI systems, and performance enhancement is less dependent on the manipulation of the system’s external, visual stimulus parameters. Secondly, we propose an ERP system that classifies the brain state as intended or unintended by considering the measurable differences between passively gazing and actively performing the pitch-imagery tasks in the EEG signal thus minimizing unintended commands to the BCI system.