Miracle-dz/UniFAR-FTUs huggingface dataset:
Species-specific PCR assay for the detection of Babesia odocoilei

We developed a PCR assay for the detection of Babesia odocoilei based on the 18S rRNA gene. Multiple specimens of B. odocoilei were examined, and the assay consistently produced a small specific PCR product of 306 bp. The PCR assay was also challenged with DNA from 13 other Babesia species and 2 Theileria species, originating from 10 different host species; however, nonspecific DNA amplification and multiple banding patterns were observed, and the amplicon banding patterns varied between different isolates of the same species. Sensitivity was determined to be 6.4 pg of DNA, and an estimated 0.0001% parasitism. This assay can be utilized for species-specific differential detection of B. odocoilei.
Idiosyncratic Tower of Babel: Individual Differences in Word-Meaning Representation Increase as Word Abstractness Increases

Humans primarily rely on language to communicate, on the basis of a shared understanding of the basic building blocks of communication: words. Do we mean the same things when we use the same words? Although cognitive neural research on semantics has revealed the common principles of word-meaning representation, the factors underlying the potential individual variations in word meanings are unknown. Here, we empirically characterized the intersubject consistency of 90 words across 20 adult subjects (10 female) using both behavioral measures (rating-based semantic-relationship patterns) and neuroimaging measures (word-evoked brain activity patterns). Across both the behavioral and neuroimaging experiments, we showed that the magnitude of individual disagreements on word meanings could be modeled on the basis of how much language or sensory experience is associated with a word and that this variation increases with word abstractness. Uncovering the cognitive and neural origins of word-meaning disagreements across individuals has implications for potential mechanisms to modulate such disagreements.
Characterization of cell cycle and apoptosis in Chinese hamster ovary cell culture using flow cytometry for bioprocess monitoring

Chinese hamster ovary (CHO) cells are by far the most important mammalian cell lines used for producing antibodies and other therapeutic proteins. It is critical to fully understand their physiological conditions during a bioprocess in order to achieve the highest productivity and the desired product quality. Flow cytometry technology possesses unique advantages for measuring multiple cellular attributes for a given cell and examining changes in cell culture heterogeneity over time that can be used as metrics for enhanced process understanding and control strategy. Flow cytometry‐based assays were utilized to examine the progression of cell cycle and apoptosis in three case studies using different antibody‐producing CHO cell lines in both fed‐batch and perfusion bioprocesses. In our case studies, we found that G0/G1 phase distribution and early apoptosis accumulation responded to subtle changes in culture conditions, such as pH shifting or momentary glucose depletion. In a perfusion process, flow cytometry provided an insightful understanding of the cell physiological status under a hypothermic condition. More importantly, these changes in cell cycle and apoptosis were not detected by a routine trypan blue exclusion‐based cell counting and viability measurement. In summary, integration of flow cytometry into bioprocesses as a process analytical technology tool can be beneficial for establishing optimum process conditions and process control.
Evaluation and screening of elite wheat germplasm for salinity stress at the seedling phase.

Salinity is one of the most important constraints for global cereal production, and breeding for salinity tolerance is a challenge. The limited gene pools, merged information regarding osmotic stress/tissue tolerance mechanism(s) including the accumulation of Na+ , over-stressed on the Na+ exclusion mechanism, and inadequate suitable screening methods further weaken the progress. In the present study, anwas made to evaluate the salt tolerance in Triticum aestivum lines using the membership function value (MFV) of certain traits viz., the root and shoot length (RL & SL), shoot and root fresh weight (SFW & RFW), shoot and root dry weight (SDW & RDW) and germination percentage (GP). This study screened 314 wheat lines (278 linked top cross population (LTPs) and 36 normal wheat cultivars) under lab conditions to evaluate their salt tolerance. A positive, and the highest, correlation coefficient was recorded between salt tolerance index (STI) of SL and the STI of RL.11 highly salt tolerant (HST), 59 salt tolerant (ST), 100 moderately salt tolerant (MST), 137 salt sensitive (SS), and 7 highly salt sensitive (HSS) were observed with a distance of 2.2 between each category. The R-square value was maximum (0.836) between the STI of SFW and the mean MFV,which can be used as the most reliable trait for the salinity tolerance in T. aestivum at the germination phase. Wheat tolerant lines had higher tolerance to salt stress in comparison with the used normal wheat cultivars were detected at the seedling stage. This article is protected by copyright. All rights reserved.
Market forces determine the distribution of a leaky function in a simple microbial community

Significance Natural microbial communities are often deeply interdependent despite being locked in competition over a small number of limiting resources. While there are theories about how evolution can generate these dependencies, less is known about how responsibility for different tasks is assigned in a community. Here, we show that even small differences in costs paid by a species for performing a vital but “leaky” function can lead to one species consistently evolving into the sole “helper” for the entire community. We suggest that this process is analogous to the human economic principle of comparative advantage, selecting for efficient divisions of labor in microbial marketplaces. Many biological functions are leaky, and organisms that perform them contribute some of their products to a community “marketplace” in which nonperforming individuals may compete for them. Leaky functions are partitioned unequally in microbial communities, and the evolutionary forces determining which species perform them and which become beneficiaries are poorly understood. Here, we demonstrate that the market principle of comparative advantage determines the distribution of a leaky antibiotic resistance gene in an environment occupied by two “species”—strains of Escherichia coli growing on mutually exclusive resources and thus occupying separate niches. Communities comprised of antibiotic-resistant cells were rapidly invaded by sensitive cells of both types. While the two phenotypes coexisted stably for 500 generations, in 15/18 replicates, antibiotic sensitivity became fixed in one species. Fixation always occurred in the same species despite both species being genetically identical except for their niche-defining mutation. In the absence of antibiotic, the fitness cost of resistance was identical in both species. However, the intrinsic resistance of the species that ultimately became the sole helper was significantly lower, and thus its reward for expressing the resistance gene was higher. Opportunity cost of resistance, not absolute cost or efficiency of antibiotic removal, determined which species became the helper, consistent with the economic theory of comparative advantage. We present a model that suggests that this market-like dynamic is a general property of Black Queen systems and, in communities dependent on multiple leaky functions, could lead to the spontaneous development of an equitable and efficient division of labor.
Cend1 and Neurog2 efficiently reprogram human cortical astrocytes to neural precursor cells and induced-neurons.

Direct reprogramming of glial cells into induced-neurons is a promising strategy for CNS repair after acute injury or neurodegenerative diseases. Grey matter astrocytes, which exhibit features of neural stem cells when activated, are an ideal cell source for direct neuronal conversion. Aim of the study is the investigation of the neuronal reprogramming capacity of CEND1 and/or Neurogenin-2 (NEUROG2) upon their overexpression on primary human adult cortical astrocytes. Our data indicate that adult human cortical astrocytes can be directly reprogrammed by either CEND1 or NEUROG2 to cells with differentiated neuronal morphology, exhibiting long neurites and branched processes. Exploration of gene expression dynamics along the conversion process revealed that neuronal genes are significantly up-regulated while astrocytic genes are down-regulated. Differentiated induced-neurons (iNs) exhibit either GABAergic or glutamatergic/dopaminergic identity upon CEND1 and NEUROG2 overexpression respectively. Co-expression of CEND1 and NEUROG2 in double-transduced cultures induced elevated expression levels of neural progenitor/stem genes and appearance of highly proliferative spheres with neural progenitor cell (NPC) properties in culture.
Interpretability-Based Multimodal Convolutional Neural Networks for Skin Lesion Diagnosis

Skin lesion diagnosis is a key step for skin cancer screening, which requires high accuracy and interpretability. Though many computer-aided methods, especially deep learning methods, have made remarkable achievements in skin lesion diagnosis, their generalization and interpretability are still a challenge. To solve this issue, we propose an interpretability-based multimodal convolutional neural network (IM-CNN), which is a multiclass classification model with skin lesion images and metadata of patients as input for skin lesion diagnosis. The structure of IM-CNN consists of three main paths to deal with metadata, features extracted from segmented skin lesion with domain knowledge, and skin lesion images, respectively. We add interpretable visual modules to provide explanations for both images and metadata. In addition to area under the ROC curve (AUC), sensitivity, and specificity, we introduce a new indicator, an AUC curve with a sensitivity larger than 80% (AUC_SEN_80) for performance evaluation. Extensive experimental studies are conducted on the popular HAM10000 dataset, and the results indicate that the proposed model has overwhelming advantages compared with popular deep learning models, such as DenseNet, ResNet, and other state-of-the-art models for melanoma diagnosis. The proposed multimodal model also achieves on average 72% and 21% improvement in terms of sensitivity and AUC_SEN_80, respectively, compared with the single-modal model. The visual explanations can also help gain trust from dermatologists and realize man–machine collaborations, effectively reducing the limitation of black-box models in supporting medical decision making.
Application of thromboelastography in comparing coagulation difference of rivaroxaban and enoxaparin for thromboprophylaxis after total hip arthroplasty

Purpose: The purpose of this study was to compare the coagulation difference in patients with either rivaroxaban or enoxaparin as thromboprophylaxis after total hip arthroplasty (THA) regarding thromboelastography (TEG) and routine coagulation tests. Patients and methods: Two hundred and twenty-eight patients undergoing primary THA were recruited in this study. They were divided into two groups according to a computer-generated random sequence. Patients in the rivaroxaban group received 10 mg of rivaroxaban orally once daily. Patients in the enoxaparin group received 4000 AxaIU (0.4 mL) of enoxaparin subcutaneously once daily. Rivaroxaban and enoxaparin were started 6–8 h after surgery. The administration of the anticoagulant prophylaxis was lasted for a minimum of 14 days. TEG and routine coagulation tests were performed on the day before the operation and 1 day and 7 days after the operation. Results: No difference was observed in the incidence of deep vein thrombosis (DVT) or pulmonary embolism (PE) between the two groups. There was no significant difference with regard to prothrombin time (PT), activated partial thromboplastin time (PTT), international normalized ratio (INR), and thrombin time (TT) between the two groups. However, while considering TEG, R time of the rivaroxaban group was significantly higher than that of the enoxaparin group (p = 0.003), whereas the maximum amplitude (MA) (p = 0.036) value and coagulation index (CI) (p = 0.002) value were significantly lower than those of the enoxaparin group. Conclusion: With regard to TEG analysis, there was coagulation difference in patients with rivaroxaban and those with enoxaparin as thromboprophylaxis after THA. Under recommended dose of rivaroxaban and enoxaparin, patients undergoing THA were in hypercoagulability on 7days postoperative.
Impact of Timing of Tocilizumab Use in Hospitalized Patients With SARS-CoV-2 Infection

BACKGROUND: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to be a global challenge due to the lack of definitive treatment strategies. We sought to determine the efficacy of early administration of anti-interleukin 6 therapy in reducing hospital mortality and progression to mechanical ventilation. METHODS: This was a retrospective chart review of 11,512 patients infected with SARS-CoV-2 who were admitted to a New York health system from March to May 2020. Tocilizumab was administered to subjects at the nasal cannula level of oxygen support to maintain an oxygen saturation of >88%. The Charlson comorbidity index was used as an objective assessment of the burden of comorbidities to predict 10-year mortality. The primary outcome of interest was hospital mortality. Secondary outcomes were progression to mechanical ventilation; the prevalence of venous thromboembolism and renal failure; and the change in C-reactive protein, D-dimer, and ferritin levels after tocilizumab administration. Propensity score matching by using a 1:2 protocol was used to match the tocilizumab and non-tocilizumab groups to minimize selection bias. The groups were matched on baseline demographic characteristics, including age, sex, and body mass index; Charlson comorbidity index score; laboratory markers, including ferritin, D-dimer, lactate dehydrogenase, and C-reactive protein values; and the maximum oxygen requirement at the time of tocilizumab administration. Mortality outcomes were evaluated based on the level of oxygen requirement and the day of hospitalization at the time of tocilizumab administration. RESULTS: The overall hospital mortality was significantly reduced in the tocilizumab group when tocilizumab was administered at the nasal cannula level (10.4% vs 22.0%; P = .002). In subjects who received tocilizumab at the nasal cannula level, the progression to mechanical ventilation was reduced versus subjects who were initially on higher levels of oxygen support (6.3% vs 18.7%; P < .001). There was no improvement in mortality when tocilizumab was given at the time of requiring non-rebreather, high-flow nasal cannula, noninvasive ventilator, or invasive ventilator. CONCLUSIONS: Early use of anti-interleukin 6 therapy may be associated with improved hospital mortality and reduction in progression to more severe coronavirus disease 2019.
Cord‐blood respiratory syncytial virus antibodies and respiratory health in first 5 years of life

To determine the potential longer‐term effects of maternal antenatal respiratory syncytial virus (RSV) vaccination, we examined the association between cord‐blood RSV‐neutralizing antibodies (RSV‐NA) and RSV infections in the first 2 years of life, RSV‐NA at 3 years, and respiratory health to age 5 years.
Evolution of a Cytoplasmic Determinant: Evidence for the Biochemical Basis of Functional Evolution of the Novel Germ Line Regulator Oskar

Abstracts Germ line specification is essential in sexually reproducing organisms. Despite their critical role, the evolutionary history of the genes that specify animal germ cells is heterogeneous and dynamic. In many insects, the gene oskar is required for the specification of the germ line. However, the germ line role of oskar is thought to be a derived role resulting from co-option from an ancestral somatic role. To address how evolutionary changes in protein sequence could have led to changes in the function of Oskar protein that enabled it to regulate germ line specification, we searched for oskar orthologs in 1,565 publicly available insect genomic and transcriptomic data sets. The earliest-diverging lineage in which we identified an oskar ortholog was the order Zygentoma (silverfish and firebrats), suggesting that oskar originated before the origin of winged insects. We noted some order-specific trends in oskar sequence evolution, including whole gene duplications, clade-specific losses, and rapid divergence. An alignment of all known 379 Oskar sequences revealed new highly conserved residues as candidates that promote dimerization of the LOTUS domain. Moreover, we identified regions of the OSK domain with conserved predicted RNA binding potential. Furthermore, we show that despite a low overall amino acid conservation, the LOTUS domain shows higher conservation of predicted secondary structure than the OSK domain. Finally, we suggest new key amino acids in the LOTUS domain that may be involved in the previously reported Oskar−Vasa physical interaction that is required for its germ line role.
Generalizability and Transportability of the National Lung Screening Trial Data: Extending Trial Results to Different Populations

Background: Randomized controlled trials (RCT) play a central role in evidence-based healthcare. However, the clinical and policy implications of implementing RCTs in clinical practice are difficult to predict as the studied population is often different from the target population where results are being applied. This study illustrates the concepts of generalizability and transportability, demonstrating their utility in interpreting results from the National Lung Screening Trial (NLST). Methods: Using inverse-odds weighting, we demonstrate how generalizability and transportability techniques can be used to extrapolate treatment effect from (i) a subset of NLST to the entire NLST population and from (ii) the entire NLST to different target populations. Results: Our generalizability analysis revealed that lung cancer mortality reduction by LDCT screening across the entire NLST [16% (95% confidence interval [CI]: 4–24)] could have been estimated using a smaller subset of NLST participants. Using transportability analysis, we showed that populations with a higher prevalence of females and current smokers had a greater reduction in lung cancer mortality with LDCT screening [e.g., 27% (95% CI, 11–37) for the population with 80% females and 80% current smokers] than those with lower prevalence of females and current smokers. Conclusions: This article illustrates how generalizability and transportability methods extend estimation of RCTs' utility beyond trial participants, to external populations of interest, including those that more closely mirror real-world populations. Impact: Generalizability and transportability approaches can be used to quantify treatment effects for populations of interest, which may be used to design future trials or adjust lung cancer screening eligibility criteria.
Molecular diversity of diencephalic astrocytes reveals adult astrogenesis regulated by Smad4

Astrocytes regulate brain‐wide functions and also show region‐specific differences, but little is known about how general and region‐specific functions are aligned at the single‐cell level. To explore this, we isolated adult mouse diencephalic astrocytes by ACSA‐2‐mediated magnetic‐activated cell sorting (MACS). Single‐cell RNA‐seq revealed 7 gene expression clusters of astrocytes, with 4 forming a supercluster. Within the supercluster, cells differed by gene expression related to ion homeostasis or metabolism, with the former sharing gene expression with other regions and the latter being restricted to specific regions. All clusters showed expression of proliferation‐related genes, and proliferation of diencephalic astrocytes was confirmed by immunostaining. Clonal analysis demonstrated low level of astrogenesis in the adult diencephalon, but not in cerebral cortex grey matter. This led to the identification of Smad4 as a key regulator of diencephalic astrocyte in vivo proliferation and in vitro neurosphere formation. Thus, astrocytes show diverse gene expression states related to distinct functions with some subsets being more widespread while others are more regionally restricted. However, all share low‐level proliferation revealing the novel concept of adult astrogenesis in the diencephalon.
Influence of Single Bouts of Aerobic Exercise on Dual-Tasking Performance in Healthy Adults

Abstract Dual-tasking performance (DTP) is critical for most real-life activities. Interventions to improve DTP would be clinically valuable. This study investigated effects of single-bouts of two different aerobic exercises on the performance of Extended cognitive Timed-Up and Go (ETUGcog), a dual-task test involving concurrent performance of a physical (ETUG) and cognitive (counting backwards serial 7 s) task. Twenty-two adults performed single bouts of high-intensity interval training (HIIT) and moderate-intensity exercise (MIE), separately. ETUGcog was performed before, immediately following, and 24 hours after each exercise. Number and rates of correct serial 7 s were significantly higher 24 hours after HIIT, with no difference in times to complete ETUGcog. No such effects were found for MIE. Single bouts of HIIT could provide delayed improvements in DTP.
Dynamics underlying auditory‐object‐boundary detection in primary auditory cortex

Auditory object analysis requires the fundamental perceptual process of detecting boundaries between auditory objects. However, the dynamics underlying the identification of discontinuities at object boundaries are not well understood. Here, we employed a synthetic stimulus composed of frequency‐modulated ramps known as ‘acoustic textures’, where boundaries were created by changing the underlying spectrotemporal statistics. We collected magnetoencephalographic (MEG) data from human volunteers and observed a slow (<1 Hz) post‐boundary drift in the neuromagnetic signal. The response evoking this drift signal was source localised close to Heschl's gyrus (HG) bilaterally, which is in agreement with a previous functional magnetic resonance imaging (fMRI) study that found HG to be involved in the detection of similar auditory object boundaries. Time–frequency analysis demonstrated suppression in alpha and beta bands that occurred after the drift signal.
Low-temperature grown vertically aligned carbon nanotube array for an optimal infrared bolometer

Vertically aligned carbon nanotube (VACNT) arrays have been explored as an absorber of thermal-type photodetectors. A long and dense VACNT array absorbs a wide spectral range of incident light with high absorption rate, but has a high thermal mass that results in a low response speed. To achieve a small thermal mass, a shorter and less dense VACNT array is needed. In addition, the high temperature needed to grow the VACNTs is detrimental to the functional sensing materials of the photodetector. The height, density, and growth temperature of VACNTs need to be optimized to achieve a working absorber that has high absorption rate and a high response speed. In this work, a low-temperature plasma enhanced chemical vapor deposition process is used to prepare various VACNT arrays with different heights and densities by controlling the CNT growth parameters. The absorption coefficients of the resulting samples are measured with Fourier transform infrared spectroscopy. An effective medium theory (EMT) is adopted to establish a working model of the VACNTs. Using experimentally extracted CNT density and height as fitting parameters, the EMT model is fitted to obtain theoretical absorption coefficients, which are found to be comparable to the experimentally measured absorption coefficients. Our experimental and theoretical investigations pave the way for future studies to integrate CNTs with infrared photodetectors.