Miracle-dz/UniFAR-FTUs huggingface dataset:
The Relationship between Changes in Organ-Tissue Mass and Sleeping Energy Expenditure Following Weight Change in College Sumo Wrestlers

Background and objectives: It has been well established that the resting energy expenditure (REE) for the whole body is the sum of the REE for each organ-tissue in young and middle-aged healthy adults. Based on these previous studies, although it is speculated that sleeping energy expenditure (SEE, which has small inter-individual variability) changes with a commensurate gain or reduction in the resting metabolic rate of each organ-tissue, it is unclear whether a change in organ-tissue masses is directly attributed to the fluctuation of SEE at present. This study aimed to assess the relationship between changes in organ-tissue mass and sleeping energy expenditure (SEE) following weight change in college Sumo wrestlers. This included blood analysis, which is related to energy expenditure. Materials and Methods: A total of 16 healthy male college Sumo wrestlers were recruited in this study. All measurements were obtained before and after weight change. Magnetic resonance imaging measurements were used to determine the volume of the skeletal muscle (SM), liver, and kidneys, and an indirect human calorimeter was used to determine SEE before and after weight change. Results: The change in body mass and SEE ranged between −8.7~9.5 kg, and −602~388 kcal/day. Moreover, changes in SM, liver, and kidneys ranged between −3.3~3.6 kg, −0.90~0.77 kg, and −0.12~0.07 kg. The change in SEE was not significantly correlated with the change in SM or liver mass, nor with blood analyses; however, a significant relationship between the change in kidney mass and SEE was observed. Conclusions: Based on our results, there is a possibility that the mass of the kidneys has an effect on the change in SEE following weight change in college Sumo wrestlers.
Proximate and Mineral Compositions of Common Crab Species [Callinectes pallidus and Cardisoma armatum] of Badagry Creek, Nigeria

Callinectes pallidus and Cardisoma armatum species were obtained at Badagry creek near to Ojo, Lagos. The proximate and mineral compositions (meats and bony tissue) of Callinectes pallidus and Cardisoma armatum crabs from Badagry Creek were analyzed, the mean body weight were 145.22 ± 3.39 and 104.47 ± 2.50 respectively. Big cheliped weight, small cheliped weight, visceral weight and leg weight were not significantly different (P 0.05), both crabs were high in calcium, potassium, magnesium, and manganese. Zinc in meat of both crabs were not significantly different (P 0.05), iron and zinc of shell of both crabs were also significantly different (P>0.05). The proximate and mineral compositions of both species of crab showed highly nutritious meat to warrant introduction into the culture system of the country to further diversify the aquaculture base of the industry presently dominated by catfish.
Predicting Cytotoxicity of Metal Oxide Nanoparticles Using Isalos Analytics Platform

A literature curated dataset containing 24 distinct metal oxide (MexOy) nanoparticles (NPs), including 15 physicochemical, structural and assay-related descriptors, was enriched with 62 atomistic computational descriptors and exploited to produce a robust and validated in silico model for prediction of NP cytotoxicity. The model can be used to predict the cytotoxicity (cell viability) of MexOy NPs based on the colorimetric lactate dehydrogenase (LDH) assay and the luminometric adenosine triphosphate (ATP) assay, both of which quantify irreversible cell membrane damage. Out of the 77 total descriptors used, 7 were identified as being significant for induction of cytotoxicity by MexOy NPs. These were NP core size, hydrodynamic size, assay type, exposure dose, the energy of the MexOy conduction band (EC), the coordination number of the metal atoms on the NP surface (Avg. C.N. Me atoms surface) and the average force vector surface normal component of all metal atoms (v⊥ Me atoms surface). The significance and effect of these descriptors is discussed to demonstrate their direct correlation with cytotoxicity. The produced model has been made publicly available by the Horizon 2020 (H2020) NanoSolveIT project and will be added to the project’s Integrated Approach to Testing and Assessment (IATA).
Cohort profile: gastric cancer in the population-based, Finnish National Esophago-Gastric Cancer Cohort (FINEGO) Study

Purpose The Finnish National Esophago-Gastric Cancer Cohort (FINEGO) was established with the aim of identifying factors that could contribute to improved outcomes in oesophago-gastric cancer. The aim of this study is to describe the patients with gastric cancer included in FINEGO. Participants A total of 10 457 patients with gastric cancer or tumour diagnosis in the Finnish Cancer Registry or the Finnish Patient Registry during 1987–2016 were included in the cohort, with follow-up from Causes of Death Registry until 31 December 2016. All of the participants were at least 18 years of age, and had undergone either resectional or endoscopic mucosal surgery with curative or palliative intent. Findings to date Of the 10 457 patients, 90.1% were identified to have cancer in both cancer and patient registries. In all, the median age was 70 at the time of surgery, 54.5% of the patients were men and 64.4% had no comorbidities. Education data were available for 31.1% of the patients, of whom the majority had had <12 years of formal education. Of the 7798 with cancer staging data available, 41.1% had a local cancer. Adenocarcinoma was the most common (94.2%) histological type. Almost all patients underwent open gastrectomy and 214% in hospitals with annual volume of more than 30 gastrectomies per year. A total of 8561 deaths occurred during the study period, of which 6474 were due to oesophago-gastric cancers. The 5-year survival was 34.6% and 5-year cancer-specific survival was 39.7%. Future plans The data in FINEGO can be currently used for registry-based research but is being expanded by data extraction from patient records and scanning of histological samples from the Finnish biobanks. Initially, we are planning on studies on the national trends in treatment and mortality, and studies on the demographic factors and their influence on survival.
MtCEP1 peptides regulate lateral organ development in the model legume, Medicago truncatula

Plant signalling peptides have been shown to have important roles in plant development. These peptides mediate signal transduction pathways that regulate specific developmental events including meristem development and cellular differentiation. In this thesis, a member of the C- terminally Encoded Peptide (CEP) family of regulatory peptides, MtCEP1, is studied in the model legume, Medicago truncatula, for its regulation of nitrogen-mediated root development, most particularly, lateral root and nodule formation. The MtCEP1 peptide-encoding gene is upregulated by low nitrogen condition, an environmental cue which strongly regulates both lateral root and nodule formation. Therefore, MtCEP1 provides an excellent research avenue as an important regulatory molecule for modulating root architecture in response to exogenous nitrogen levels. In this thesis, I have functionally characterized MtCEP1 for its role in regulating lateral root and nodule development. This is the first characterization of a CEP peptide member in Medicago and outside of Arabidopsis. MtCEP1 negatively regulates lateral root formation and promotes nodulation. There are three characteristic root phenotypes when MtCEP1 was overrepresented to the root (either by overexpressing the peptide-encoding gene or applying the synthetic peptide to the root): (1) reduction of lateral root number, (2) increased in nodulation competency and nodule number, (3) formation of periodic circumferential cell proliferation (CCP) sites. By knocking down MtCEP1 using a multigene RNAi construct to reduce gene redundancy effects, significantly more lateral roots were formed while there was no change in the nodule number. This corroborates the results with MtCEP1 promoter analysis using GUS reporter construct (pMtCEP1:GUS) which showed high expression in lateral root primordia when grown in low nitrogen condition. These results suggest the direct regulation of MtCEP1 in regulating lateral roots. Nonetheless, pMtCEP1:GUS also displayed high expression in young nodule primordia indicating that MtCEP1 could be indirectly regulating nodulation by modulating the root nodulation susceptibility during nitrogen limitation. Analysis of the nodule phenotypes revealed wider zone of susceptibility to nodulation, increased nodule number and nodule morphologies akin to ethylene-insensitive mutant, sickle. Therefore, this thesis further explores MtCEP1 regulation of nodule development, focusing on ethylene-mediated pathway. In Medicago, ethylene regulates nodulation susceptibility and provides positional information for nodulation. In the sickle mutant, a mutant of the EIN2 (ETHYLENE INSENSITIVE 2) in the ethylene signaling pathway, hypernodulation and loss of positional information of the nodules could be observed. By utilizing the sickle mutant, I have demonstrated in…
COVID-19 observations and accompanying dataset of non-pharmaceutical interventions across U.S. universities, March 2020

Background The Centers for Disease Control and Prevention (CDC) publishes COVID-19 non-pharmaceutical intervention (NPI) guidance for specific institutional audiences to limit community spread. Audiences include: business, clinical, public health, education, community, and state/local government. The swift, severe, and global nature of COVID-19 offers an opportunity to systematically obtain a national view of how larger institutions of higher education adopted NPI guidance at the onset of the pandemic. Method An original database of COVID-19-related university NPI policy changes was compiled. Survey team members manually combed university websites and official statements capturing implementation decisions and dates for five NPI variables from 575 U.S. universities, across 50 states and the District of Columbia, during March of 2020. The universities included in this study were selected from the Department of Education Integrated Postsecondary Education Data System (IPEDS), which provides a set of university explanatory variables. Using IPEDS as the basis for the organizational data allows consistent mapping to event-time and institutional characteristic variables including public health announcements, geospatial, census, and political affiliation. Results The dataset enables event-time analysis and offers a variety of variables to support institutional level study and identification of underlying biases like educational attainment. A descriptive analysis of the dataset reveals that there was substantial heterogeneity in the decisions that were made and the timing of these decisions as they temporally related to key state, national, and global emergency announcements. The WHO pandemic declaration coincided with the largest number of university decisions to implement NPIs. Conclusion This study provides descriptive observations and produced an original dataset that will be useful for future research focused on drivers and trends of COVID-19 NPIs for U.S. Universities. This preliminary analysis suggests COVID-19 university decisions appeared to be made largely at the university level, leading to major variations in the nature and timing of the responses both between and within states, which requires further study.
The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity

The Ccr4-Not complex functions as an effector of multiple signaling pathways that control gene transcription and mRNA turnover. Consequently, Ccr4-Not contributes to a diverse array of processes, which includes a significant role in cell metabolism. Yet a mechanistic understanding of how it contributes to metabolism is lacking. Herein, we provide evidence that Ccr4-Not activates nutrient signaling through the essential target of rapamycin complex 1 (TORC1) pathway. Ccr4-Not disruption reduces global TORC1 signaling, and it also upregulates expression of the cell wall integrity (CWI) pathway terminal kinase Mpk1. Although CWI signaling represses TORC1 signaling, we find that Ccr4-Not loss inhibits TORC1 independently of CWI activation. Instead, we demonstrate that Ccr4-Not promotes the function of the vacuole V-ATPase, which interacts with the Gtr1 GTPase-containing EGO complex to stimulate TORC1 in response to nutrient sufficiency. Bypassing the V-ATPase requirement in TORC1 activation using a constitutively active Gtr1 mutant fully restores TORC1 signaling in Ccr4-Not deficient cells. Transcriptome analysis and functional studies revealed that loss of the Ccr4 subunit activates the TORC1 repressed retrograde signaling pathway to upregulate mitochondrial activity. Blocking this mitochondrial upregulation in Ccr4-Not deficient cells further represses TORC1 signaling, and it causes synergistic deficiencies in mitochondrial-dependent metabolism. These data support a model whereby Ccr4-Not loss impairs V-ATPase dependent TORC1 activation that forces cells to enhance mitochondrial metabolism to sustain a minimal level of TORC1 signaling necessary for cell growth and proliferation. Therefore, Ccr4-Not plays an integral role in nutrient signaling and cell metabolism by promoting V-ATPase dependent TORC1 activation.
Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the pre-vaccine period. Therefore, Rotarix® did not appear to have an impact on the amino acid differences in the antigenic regions of South African post-vaccine G1P[8] strains. However, continued whole-genome surveillance of RVA strains to decipher genetic changes in the post-vaccine period remains imperative.
The clinicopathological features and prognosis of primary pulmonary lymphoepithelioma-like carcinoma: A systematic review and meta-analysis

Background Primary pulmonary lymphoepithelioma-like carcinoma (PPLELC) was a sparse subtype of unclassified lung cancer. The clinicopathologic features, prognostic factors and multimodality treatment regimens of LELC remain inconclusive. We conducted this systematic review and meta-analysis to address this deficit in current knowledge. Methods We searched PubMed, Embase, and Web of Science to filtrate studies investigating on clinical features and prognostic factors of LELC up to Sep 9th, 2020. Fixed and random effect models were generated to present the incorporated hazard ratios (HR) and odds ratios (OR) with 95% confidence intervals (CI). The quality and heterogeneity of the included studies were also evaluated carefully. Results This systematic review and meta-analysis included 13 retrospective studies with a total of 1294 patients. The incidence of programmed cell death-ligand 1 (PD-L1) expression in PPLELC varied from 63.3% to 75.8%. Positive PD-L1 expression was more likely to be found in patients under 60 years old (OR = 2.16, 95%CI: 1.19–3.89, P = 0.01) and was associated with worse disease-free survival (DFS) compared with negative PD-L1 expression (HR = 2.99, 95%CI: 1.23–7.28, P = 0.02). The pooled results showed that stage was the prognostic factor for both overall survival (OS) and DFS. Moreover, a significantly better outcome of PPLELC was observed in men (HR = 0.56, 95%CI: 0.33–0.95, P = 0.03) and patients who received radiation (HR = 0.46, 95%CI: 0.22–0.96, P = 0.04). Conclusion PD-L1 expression was high in PPLELC patients. It was significantly associated with age under 60 and the unfavorable DFS. Stage and gender could be the prognostic factor for OS. Radiation could be the effective therapy for PPLELC.
Night-time nurturing : an evolutionary perspective on breastfeeding and sleep.

Consideration of the phylogenetic depth and cross-cultural breadth of mother–infant biology and behavior illuminates contemporary infant care. Three key “ancestral environments” (AEs) have defined the care requirements of newborn humans (lactation, frequent suckling, and maternal close contact). These evolved requirements have been challenged by various “new cultural environments” (NCEs) propelling infant care in directions that are incongruent with evolved maternal and infant biology (e.g., postpartum separation of mothers and infants, widespread acceptance of nonhuman milk feeding). As a consequence, over the past century, infant feeding and sleeping have become decoupled from the mother's body—with far-reaching ramifications.
Staphylococcus aureus and Methicillin Resistant S. aureus in Nepalese Primates: Resistance to Antimicrobials, Virulence, and Genetic Lineages

Staphylococcus aureus is a ubiquitous pathogen and colonizer in humans and animals. There are few studies on the molecular epidemiology of S. aureus in wild monkeys and apes. S. aureus carriage in rhesus macaques (Macaca mulatta) and Assam macaques (Macaca assamensis) is a species that has not previously been sampled and lives in remote environments with limited human contact. Forty Staphylococcus aureus isolates including 33 methicillin-susceptible S. aureus (MSSA) and seven methicillin-resistant S. aureus (MRSA) were characterized. Thirty-four isolates were from rhesus macaques and six isolates (five MSSA, one MRSA) were from Assam macaques. Isolates were characterized using StaphyType DNA microarrays. Five of the MRSA including one from Assam macaque were CC22 MRSA-IV (PVL+/tst+), which is a strain previously identified in Nepalese rhesus. One MRSA each were CC6 MRSA-IV and CC772 MRSA-V (PVL+). One MSSA each belonged to CC15, CC96, and CC2990. Six MRSA isolates carried the blaZ, while ten known CC isolates (seven MRSA, three MSSA) carried a variety of genes including aacA-aphD, aphA3, erm(C), mph(C), dfrA, msrA, and/or sat genes. The other 30 MSSA isolates belonged to 17 novel clonal complexes, carried no antibiotic resistance genes, lacked Panton–Valentine Leukocidin (PVL), and most examined exotoxin genes. Four clonal complexes carried egc enterotoxin genes, and four harbored edinB, which is an exfoliative toxin homologue.
Diatom modulation of select bacteria through use of two unique secondary metabolites

Significance Phytoplankton are major primary producers in the marine environment that excrete a wide range of metabolites. These exudates support the growth of surrounding bacteria that in turn provide phytoplankton cells with resources and growth cofactors to proliferate. Unlike multicellular eukaryotes with dedicated structures housing microbiomes, mechanisms enabling unicellular eukaryotic phytoplankton hosts to modulate potential symbionts and opportunists within a natural microbial community are unknown. Exposure of a host phytoplankton cell to its natural microbial community triggers major transcriptional and metabolic reprogramming to release unique secondary metabolites that selectively enable growth and attachment of symbiotic taxa while simultaneously suppressing the colonization of nonsymbiont bacteria. These results suggest strong and highly selective microbiome-modulating strategies shared across the unicellular and multicellular eukaryotic lineages. Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world’s oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.
Difference of [Ca2+]i Movements in Platelets Stimulated by Thrombin and TRAP: the Involvement of αIIbβ3-Mediated TXA2 Synthesis

Summary This study investigated the difference of [Ca2+]i movement in platelets in response to thrombin and TRAP. The involvement of αIIbβ3 in this signaling was also studied. Stimulation of platelets with thrombin at 0.03 U/ml caused platelet aggregation and a two-peak increase in [Ca2+]i. The second peak of [Ca2+]i, but not the first peak was abolished by the inhibition of platelet aggregation with αIIbβ3 antagonists or by scavenging endogenous ADP with apyrase. A cyclooxygenase inhibitor, aspirin, and a TXA2 receptor antagonist, BM13505, also abolished the second peak of [Ca2+]i but not the first peak, although these regents did not inhibit aggregation. Under the same assay conditions, measurement of TXB2 demonstrated that αIIbβ3 antagonists and aspirin almost completely inhibited the production of TXB2. In contrast to thrombin-stimulation, TRAP caused only a single peak of [Ca2+]i even in the presence of platelet aggregation, and a high level of [Ca2+]i increase was needed for the induction of platelet aggregation. The inhibition of aggregation with αIIbβ3 antagonists had no effect on [Ca2+]i change and TXB2 production induced by TRAP. Inhibition studies using anti-GPIb antibodies suggested that GPIb may be involved in the thrombin response, but not in the TRAP. Our findings suggest that low dose thrombin causes a different [Ca2+]i response and TXA2 producing signal from TRAP. Endogenous ADP release and fibrinogen binding to αIIbβ3 are responsible for the synthesis of TXA2 which results in the induction of the second peak of [Ca2+]i in low thrombin- but not TRAP-stimulated platelets.