Miracle-dz/UniFAR-FTUs huggingface dataset:
Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen-Deficient Stress Condition.

The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen-stress condition. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants was used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N +) and nitrogen-deficient (N -) conditions. Model-predicted flux-sum variability analysis achieved 70% accuracy comparing to the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (L-methionine, L-asparagine, L-lysine, cholesterol, and L-pipecolate) playing regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidyl-choline and phosphatidyl-glycerol metabolites which even though not coupled with biomass production played a key role in the increased biomass production under N -. Overall, the omics-integrated-GSM provides a promising tool to facilitate stress-condition analysis for maize root and engineer better stress-tolerant maize genotypes.
Fear of Reinjury Following Anterior Cruciate Ligament Reconstruction Is Manifested in Muscle Activation Patterns of Single-Leg Side-Hop Landings

Abstract Objective The purpose of this study was to determine whether fear of re-injury is manifested in joint kinematics and muscle activation patterns during landings of a standardized rebound side-hop (SRSH), or in patient-reported outcome measures (PROMs), among individuals with anterior cruciate ligament reconstruction (ACLR). Methods In this cross-sectional observational study, 38 individuals within 2 years post-ACLR were grouped into HIGH-FEAR (n = 21, median 11.2 months post-surgery) or LOW-FEAR (n = 17, median 10.1 months post-surgery) based on a discriminating question (Q9; Tampa Scale of Kinesiophobia-17). These individuals and 39 asymptomatic controls performed the SRSH. Three-dimensional motion recordings were used to calculate trunk, hip, and knee joint angles at initial contact and range of respective joint motion during landing. Surface electromyography registered mean amplitudes and co-contraction indexes for thigh muscles during pre-activation (50 ms) and landing phases. PROMs of knee function, knee health, and physical activity were also analyzed. Results The HIGH-FEAR and LOW-FEAR classification was corroborated by distinct Tampa Scale of Kinesiophobia-17 total and subscale scores and revealed distinguishable muscle activation patterns. HIGH-FEAR demonstrated higher biceps femoris electromyography amplitude and higher anterior-posterior co-contraction index during landing than both LOW-FEAR and controls. However, there were no fear-related differences for kinematics or PROMs. Instead, both ACLR subgroups showed different kinematics at initial contact to controls; HIGH-FEAR with more trunk, hip, and knee flexion, and LOW-FEAR with more hip and knee flexion. Conclusion Individuals with ACLR who had high fear of re-injury seem to have adopted a protective strategy with higher muscular activation patterns, presumably to stabilize the knee joint, compared with individuals with low fear of re-injury and controls. SRSH landing kinematics or knee-related PROMs may not be as sensitive to fear of re-injury. Impact Fear of reinjury following anterior cruciate ligament injury should be evaluated as an independent psychological outcome throughout rehabilitation after ACLR for improved return to sport transition. Lay Summary If you have an anterior cruciate ligament injury treated with reconstructive surgery, you might have a high fear of reinjury, and that can change how you activate the muscles around your knee. Your physical therapist can do a simple screening test in addition to functional tests to help reduce your fear and improve your treatment outcomes.
Engaging the Sickle Cell Community in Participatory Research

partnership. (4) Community-based organizations (CBOs) can be hubs for community-based research independent of academic research institutions. In part this reflects the broader shift toward patient-led research and citizen-science, and community’s needs to control data, samples, and research agendas most clearly demonstrated in indigenous communities’ efforts. In an AANHPI context, it also demonstrates a need for establishing independent routes for research and funding for Native Hawaiian Pacific Islander communities.
A pig model of tunneled dialysis catheter (TDC) infection and dysfunction: Opportunities for therapeutic innovation

Background: Although tunneled dialysis catheters (TDC) are far from ideal, they still represent the main form of vascular access for most patients beginning dialysis. Catheters are easy to place and allow patients instant access to dialysis, but regardless of these benefits, catheters are associated with a high incidence of significant complications like bloodstream infections, central venous stenosis, thrombosis, and dysfunction. In the present study, we aim to describe and characterize a swine model of catheter dysfunction and bloodstream infection, that recreates the clinical scenario, to help to serve as a platform to develop therapeutic innovations for this important clinical problem. Methods: Six Yorkshire cross pigs were used in this study. Non-coated commercial catheters were implanted in the external jugular recreating the main features of common clinical practice. Catheters were aseptically accessed twice a week for a mock dialysis procedure (flushing in and out) to assess for and identify catheter dysfunction. Animals were monitored daily for infections; once detected, blood samples were collected for bacterial culture and antibiograms. Study animals were euthanized when nonresponsive to treatment. Tissue samples were collected in a standardized fashion for macroscopic inspection and histological analysis. Results: The data analysis revealed an early onset of infection with a median time to infection of 9 days, 40% of the isolates were polymicrobial, and the average time to euthanasia was 20.16 ± 7.3 days. Median time to catheter dysfunction onset was 6 days post-implantation. Postmortem dissection revealed external fibrin sheath and internal thrombosis as the main causes of catheter dysfunction. There was also evidence of central venous stenosis with positive cells for αSMA, CD68, Ki67, Smoothelin, and Vimentin within the venous neointima. Conclusions: The described model represents a reliable and reproducible large animal model of catheter dysfunction and bloodstream infection, which recreates all the main complications of TDC’s and so could be used as a validated large animal model to develop new therapies for TDC related infection, thrombosis/dysfunction and central venous stenosis.
Comparison of Clinical Outcome and Radiologic Parameters in Open TLIF Versus MIS-TLIF in Single- or Double-Level Lumbar Surgeries

ABSTRACT Purpose: The objective of this study was to compare clinical and radiologic parameters between minimally invasive surgery–transforaminal lumbar interbody fusion (MIS-TLIF) and open TLIF. Methods: Data of 145 patients who underwent single- or double-level TLIF procedures with an open (n = 76) or a MIS (n = 69) technique were analyzed. Average operation time, estimated blood loss, and hospital stay were compared between open TLIF and MIS-TLIF. Improvement in clinical scores was analyzed using visual analog scale (VAS) and Oswestry Disability Index (ODI) scores in both groups and statistically compared using t tests. Radiologic parameters, such as lumbar lordosis, focal lordosis at the index level, and pelvic incidence (PI), were calculated at preoperative, postoperative, and final follow-up for comparison. The differences in improvement between open and MIS groups were analyzed using unpaired t tests. Results: Average follow-up was 35.8 ± 15.4 months in open TLIF and 37.9 ± 14.4 months in MIS-TLIF. The average blood loss and operation times were higher and hospital stay was less in MIS-TLIF compared to open TLIF. VAS scores were improved from preoperative (8.5 ± 0.6) to postoperative (2.1 ± 0.8) and preoperative (8.4 ± 0.8) to postoperative (2.0 ± 0.7) in open TLIF and MIS-TLIF, respectively (P < .0001), and ODI scores were improved from preoperative (55.2 ± 5.2) to postoperative (22.5 ± 4.3) and preoperative (56.7 ± 4.9) to postoperative (22.0 ± 5.0) in open TLIF and MIS-TLIF, respectively (P < .0001). Similarly, there were significant improvements in lumbar lordosis and focal lordosis at the index level with a difference of 3.9° and 2.5°, respectively, in open TLIF and 4.0° and 2.9°, respectively, in MIS-TLIF. However, there were no differences in PI in both groups. There were 9 (11.8%) and 9 (13%) complications encountered in open TLIF and MIS-TLIF, respectively. Two patients from open TLIF and 5 from MIS-TLIF had to undergo revision surgeries without any statistical difference. Conclusions: Open TLIF and MIS-TLIF are equally efficient surgical techniques with similar clinical and radiologic outcomes. MIS-TLIF is associated with less intraoperative blood loss and hospital stay; however, it increases operation time significantly.
Automation of QIIME2 Metagenomic Analysis Platform

QIIME is a widely used, open‐source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets available at docs.qiime2. org. While these specific examples are microbial 16S rRNA gene sequences, our automation can be easily applied to other types of QIIME2 analysis. © 2021 Wiley Periodicals LLC.
timeOmics: an R package for longitudinal multi-omics data integration

MOTIVATION Multi-omics data integration enables the global analysis of biological systems and discovery of new biological insights. Multi-omics experimental designs have been further extended with a longitudinal dimension to study dynamic relationships between molecules. However, methods that integrate longitudinal multi-omics data are still in their infancy. RESULTS We introduce the R package timeOmics, a generic analytical framework for the integration of longitudinal multi-omics data. The framework includes pre-processing, modelling and clustering to identify molecular features strongly associated with time. We illustrate this framework in a case study to detect seasonal patterns of mRNA, metabolites, gut taxa, and clinical variables in patients with diabetes mellitus from the integrative Human Microbiome Project. AVAILABILITY timeOmics is available on Bioconductor and github.com/abodein/timeOmics.
Effects of Rosmarinus officinalis on orchitis following spermatic cord torsion‐detorsion in male mice with emphasis on anti‐ inflammatory and antioxidant properties

Orchitis as inflammation of testis occurs following traumatic injuries such as testicular torsion leading to high levels of oxidative stress and inflammation. Rosmarinus officinalis is a herb with anti‐inflammatory and antioxidant properties. This study assessed therapeutic effects of rosemary following testicular torsion. A total of 36 male mice were categorised; control, torsion, rosemary (100 and 200 mg/kg) and torsion+rosemary groups. Torsion was induced surgically, and rosemary was gavaged. Total antioxidant capacity of extract was approved by Ferric Reducing Ability of Plasma. Malondialdehyde and Griess protocols were hired to assess oxidative stress. Finally, sperm parameters and testosterone levels were analysed. Immunofluorescent (of Tumour Necrosis Factor Alpha), hematoxylin and eosin stainings and expression of inflammatory genes (Interleukin‐1α, Interleukin‐1β, Interferon‐γ) were also assessed. Data were analysed using SPSS (v. 19), and graphs were drawn by GraphPad Prism (v. 9). Significantly (p < .05), oxidative stress indices and inflammatory genes expression were increased in torsion group, and total antioxidant capacity was increased in rosemary groups. In torsion+rosemary groups, total antioxidant capacity, sperm parameters and testosterone levels were increased, and inflammatory gene expression decreased significantly (p < .05). Rosemary with anti‐inflammatory and antioxidant properties accelerates testicular healing in torsion cases, especially in therapeutic dose of 200 mg/kg.
Rhizobacteria Impact Colonization of Listeria monocytogenes on Arabidopsis thaliana Roots

Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes’ existence in these settings. ABSTRACT In spite of its relevance as a foodborne pathogen, we have limited knowledge about Listeria monocytogenes in the environment. L. monocytogenes outbreaks have been linked to fruits and vegetables; thus, a better understanding of the factors influencing its ability to colonize plants is important. We tested how environmental factors and other soil- and plant-associated bacteria influenced L. monocytogenes’ ability to colonize plant roots using Arabidopsis thaliana seedlings in a hydroponic growth system. We determined that the successful root colonization of L. monocytogenes 10403S was modestly but significantly enhanced by the bacterium being pregrown at higher temperatures, and this effect was independent of the biofilm and virulence regulator PrfA. We tested 14 rhizosphere-derived bacteria for their impact on L. monocytogenes 10403S, identifying one that enhanced and 10 that inhibited the association of 10403S with plant roots. We also characterized the outcomes of these interactions under both coinoculation and invasion conditions. We characterized the physical requirements of five of these rhizobacteria to impact the association of L. monocytogenes 10403S with roots, visualizing one of these interactions by microscopy. Furthermore, we determined that two rhizobacteria (one an inhibitor, the other an enhancer of 10403S root association) were able to similarly impact 10 different L. monocytogenes strains, indicating that the effects of these rhizobacteria on L. monocytogenes are not strain specific. Taken together, our results advance our understanding of the parameters that affect L. monocytogenes plant root colonization, knowledge that may enable us to deter its association with and, thus, downstream contamination of, food crops. IMPORTANCE Listeria monocytogenes is ubiquitous in the environment, being found in or on soil, water, plants, and wildlife. However, little is known about the requirements for L. monocytogenes’ existence in these settings. Recent L. monocytogenes outbreaks have been associated with contaminated produce; thus, we used a plant colonization model to investigate factors that alter L. monocytogenes’ ability to colonize plant roots. We show that L. monocytogenes colonization of roots was enhanced when grown at higher temperatures prior to inoculation but did not require a known regulator of virulence and biofilm formation. Additionally, we identified several rhizobacteria that altered the ability of 11 different strains of L. monocytogenes to colonize plant roots. Understanding the factors that impact L. monocytogenes physiology and growth will be crucial for finding mechanisms (whether chemical or microbial) that enable its removal from plant surfaces to reduce L. monocytogenes contamination of produce and eliminate foodborne illness.
Diazinon exposure reduces bone mineral density in adult and immature rats: A histomorphometric and radiographic study

Diazinon has been widely used as a domestic and agricultural pesticide. This study examined the effects of diazinon on bone mineral density (BMD) of mature and immature rats. For this purpose, 24 adult Wistar rats (male; 8 weeks old) were initially divided into four groups (n = 6). Corn oil was used as the control while diazinon at 15, 30, and 45 mg/kg in corn oil was given to mature rats via gavage per day. Since these dosages were lethal for the immature rats, 12 immature Wistar rats (male; 4 weeks old) (n = 6) were gavaged with corn oil as control and 5 mg/kg of diazinon in corn oil. The animals were sacrificed on day 28 with their left femur bones removed for histomorphometric studies. BMD was measured in the right femur, using standardized radiographs in the femoral head, femoral neck, greater trochanter, and shaft. The Image J Program was used for measuring the bone lamellae and epiphyseal growth plates. The results of this study for the first time revealed that diazinon reduced BMD in both adults and immature rats. Diazinon exposure was associated with diminished trabecular and cortical bone density. Correspondingly, our results indicated that in immature rats, DZN led to the reduction in the epiphyseal growth plate width, both in the proliferation and hypertrophic zones. These results suggested that diazinon might be associated with impaired bone longitudinal growth as well as bone metabolism in adults.
A study of the mechanism by which bioaerosols are generated when liquids containing microorganisms are aerated

the requirements for an advanced degree from the Georgia Institute of Technology, I agree that the Library of the Institute shall make it available for inspection and circulation in accordance with its regulations governing materials of this type. I agree that permission to copy from, or to publish from, this dissertation may be granted by the professor under whose direction it was written, or, in his absence, by the Dean of the Graduate Division when such copying or publication is solely for scholarly purposes and does not involve potential financial gain. It is understood that any copying from, or publication of, this dissertation which involves potential financial gain will not be allowed without written permission.
Psychological distress, optimism and emotion regulation among Israeli Jewish and Arab pregnant women during COVID-19

ABSTRACT Background Pregnancy is a vulnerable period for women, and it is especially so under the worldwide COVID-19 pandemic. Whereas there is some evidence for distress among pregnant women during the outspread of COVID-19, little is known about the second wave of the pandemic. We therefore sought to examine the contribution of background variables, ethnicity (Jewish, Arab), personal resources (optimism, emotion regulation), and COVID-19-related anxieties to pregnant Israeli women’s psychological distress. Method A convenience sample of 1127 Israeli women was recruited from 5 July to 7 October 2020. Results Not having an academic degree, lower economic status, being an Arab woman, poorer physical health, lower levels of optimism and cognitive reappraisal, higher levels of emotion suppression and COVID-19-related anxieties all contributed significantly to greater psychological distress. Finally, ethnicity moderated the relationship between optimism and emotion suppression and the woman’s level of psychological distress. Conclusions The findings reveal risk and resilience factors associated with the psychological distress of pregnant women during the second wave of the COVID-19 pandemic and highlight the potentially greater vulnerability of women from a minority group, showing that ethnicity plays a central role in the way personal resources are related to psychological distress at such times.
Draft Genome Sequence of Streptomyces sp. Strain PAM3C, a Prospective Probiotic Agent Isolated from the Gut of the Bay Scallop, Argopecten purpuratus (Lamarck, 1819)

Several bacterial genera with antagonistic activity against pathogenic organisms have been isolated in pure culture from the gut of the Peruvian scallop, Argopecten purpuratus. One strain shows a broad inhibitory activity against aquaculture pathogenic bacterial strains. In this communication, we announce the draft genome sequence of Streptomyces sp. strain PAM3C. ABSTRACT Several bacterial genera with antagonistic activity against pathogenic organisms have been isolated in pure culture from the gut of the Peruvian scallop, Argopecten purpuratus. One strain shows a broad inhibitory activity against aquaculture pathogenic bacterial strains. In this communication, we announce the draft genome sequence of Streptomyces sp. strain PAM3C.
Effects of Allopurinol on Ketone Body Metabolism and Tissue Lipid Peroxidation in Alloxan Diabetes in Rats

The aim of the present study is to investigate whether or not xanthine oxidase (XO)â€“derived reactive oxygen species (ROS) may play a role in the pathogenesis of alloxan (ALX)â€“induced diabetes in rats using the specific XO inhibitor and hydroxyl radical scavenger, allopurinol The involvement of oxidative stress in ALX â€“ diabetes was assessed by the measurement of plasma and various tissues lipid peroxides levels ( using thiobarbituric acid ( TBA ) reactive substances ). Furthermore, the ability of allopurinol to influence these and other biochemical parameters, including plasma and urine ketones levels were also investigated in diabetic rats. Rats were divided into four groups: control, untreated diabetic, allopurinol â€“ treated diabetic, and insulin â€“ treated diabetics. At the end of the one week experimental period, blood and tissue samples were obtained from anesthesized animals for the measurement of the above â€“ mentioned parameters. Although the single intraperitoneal (i.p.) injection of allopurinol (25 mg/kg body wt.) 1h before or 1h after ALX injection (100 mg/kg body wt., i.p.) failed to prevent the induction of diabetes, it did lower ketonuria and the incidence of early ketosisâ€“associated mortality in diabetic animals in comparison with nonâ€“allopurinolâ€“treated diabetic rats. Subsequent administration of allopurinol (25 mg/kg body wt., i.p.) every 48 hr for 1wk (i.e., 3 additional doses) also decreased plasma ketone bodies levels as well as plasma and tissue (heart, liver, kidney, pancreas) lipid peroxides levels in comparison with nonâ€“allopurinolâ€“treated diabetic rats. Daily insulin injection (9â€“12 U/kg body wt., S.C.) for 1wk period normalized all of the aboveâ€“mentioned abnormalities. The present results suggest that XOâ€“derived ROS play a minor role (if any) in the diabetogenic effect of ALX. On the other hand, although the mechanism (s) underlying the protective effects of allopurinol on the diabetic state is presently unknown, these effects may reflect a possible association between impaired ketone body metabolism and lipid peroxidation: and suggest an effect of allopurinol on ketone body metabolism.