Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic factors associated with cancer racial disparity – an integrative study across twenty‐one cancer types

It is well known that different racial groups have significantly different incidence and mortality rates for certain cancers. It has been suggested that biological factors play a major role in these cancer racial disparities. Previous studies on the biological factors contributing to cancer racial disparity have generated a very large number of candidate factors, although there is modest agreement among the results of the different studies. Here, we performed an integrative analysis using genomic data of 21 cancer types from TCGA, GTEx, and the 1000 Genomes Project to identify biological factors contributing to racial disparity in cancer. We also built a companion website with additional results for cancer researchers to freely mine. Our study identified genes, gene families, and pathways displaying similar differential expression patterns between different racial groups across multiple cancer types. Among them, XKR9 gene expression was found to be significantly associated with overall survival for all cancers combined as well as for several individual cancers. Our results point to the interesting hypothesis that XKR9 could be a novel drug target for cancer immunotherapy. Bayesian network modeling showed that XKR9 is linked to important cancer‐related genes, including FOXM1, cyclin B1, and RB1CC1 (RB1 regulator). In addition, metabolic pathways, neural signaling pathways, and several cancer‐related gene families were found to be significantly associated with cancer racial disparities for multiple cancer types. Single nucleotide polymorphisms (SNPs) discovered through integrating data from the TCGA, GTEx, and 1000 Genomes databases provide biologists the opportunity to test highly promising, targeted hypotheses to gain a deeper understanding of the genetic drivers of cancer racial disparity and cancer biology in general.
Assessing conserved function of conidiation regulators in two distantly related ascomycetes, Aspergillus nidulans and Neurospora crassa

Assessing Conserved Function of Conidiation Regulators in Two Distantly Related Ascomycetes, Aspergillus nidulans and Neurospora crassa. (May 2011) Da Woon Chung, B.S., Ewha Womans University, Seoul, South Korea; M.S., Seoul National University, Seoul, South Korea; M.S., University of Wisconsin-Madison Chair of Advisory Committee: Dr. Brian D. Shaw Conidiation is a common and critical asexual reproductive mode in fungi. The ascomycetes, the largest group in the kingdom Fungi undergo conidiation. The wide array of morphological differences in conidiophores and conidial size, shape, and cellular organization demonstrates the importance of evolution in driving the morphological and functional diversity. An important unanswered question is how these conidiation processes evolve. We hypothesized that a conidiation regulatory pathway was present in the ancestral species, and became specialized in the extant species to lead to morphological and functional diversity. To address this hypothesis we assessed the conserved function of conidiation regulators in two distantly related ascomycetes, Aspergillus nidulans and Neurospora crassa. Using sequence similarity analysis, N. crassa orthologs were characterized to seven main conidiation regulatory genes in A. nidulans (fluG, flbC, flbD, abaA, wetA, medA, and stuA). Expression of the N. crassa orthologs complemented defective conidiation in the A. nidulans fluG, flbD, wetA, medA, and stuA mutants. In contrast, abaA and flbC and the N. crassa orthologs did not
Early Detection and Control of Methicillin resistant Staphylococcus aureus Outbreak in an Intensive Care Unit

Background Although Methicillin resistant Staphylococcus aureus (MRSA) is one of the major pathogens of healthcare associated infections, we had only sporadic cases in our intensive care unit (ICU) for years. Aims To investigate the sudden increase in the number of MRSA cases in ICU. Study design Descriptive study. Methods From the 5th December 2016 to 26th January 2017, we detected 11 new MRSA cases in ICU. Screening of 73 ICU healthcare workers (HCWs) and screening of 13 patients was performed for outbreak investigation. Nine clinical isolates available in stocks and eight screening MRSA isolates were included in molecular studies. PFGE, spa-mecA-mecC-PVL in-house multiplex PCR assay and spa typing, SCCmec typing were performed for all isolates. Sequence type of the representative strain was determined by Multi-Locus Sequence typing (MLST). Results All strains were mecA positive, PVL negative, and have the same antimicrobial susceptibility pattern except for two strains. All clinical, two patient screening and three nasal isolates of HCWs showed the same pulsotype, named clone A. The spa type of outbreak isolates is t030 and the SCCmec type is SCCmecIII; the MLST type of representative strain is ST239 (PFGE pulsotype A, ST239-SCCmecIII-t030). Unrelated three isolates had PFGE pulsotype B-SCCmecI-t030, PFGE pulsotype C-SCCmecIII-t459, PFGE pulsotype D-SCCmecIII. Conclusion Molecular typing techniques are the cornerstones for the investigation of outbreaks. Infection control measures, such as enhancing cleaning procedures, promoting hand hygiene, should be enforced in the ICU unit. All patients, including those who have already been discharged to other departments, must be put on contact isolation. HCWs carrying the MRSA strains could be offered decolonization.
A Bayesian hierarchical change point model with parameter constraints

Alzheimer’s disease is the leading cause of dementia among adults aged 65 or above. Alzheimer’s disease is characterized by a change point signaling a sudden and prolonged acceleration in cognitive decline. The timing of this change point is of clinical interest because it can be used to establish optimal treatment regimens and schedules. Here, we present a Bayesian hierarchical change point model with a parameter constraint to characterize the rate and timing of cognitive decline among Alzheimer’s disease patients. We allow each patient to have a unique random intercept, random slope before the change point, random change point time, and random slope after the change point. The difference in slope before and after a change point is constrained to be nonpositive, and its parameter space is partitioned into a null region (representing normal aging) and a rejection region (representing accelerated decline). Using the change point time, the estimated slope difference, and the threshold of the null region, we are able to (1) distinguish normal aging patients from those with accelerated cognitive decline, (2) characterize the rate and timing for patients experiencing cognitive decline, and (3) predict personalized risk of progression to dementia due to Alzheimer’s disease. We apply the approach to data from the Religious Orders Study, a national cohort study of aging Catholic nuns, priests, and lay brothers.
Distribution and Conservation Status of the Mount Kilimanjaro Guereza Colobus guereza caudatus Thomas, 1885

Abstract: The Mount Kilimanjaro guereza Colobus guereza caudatus is considered to be endemic to northeast Tanzania. This paper presents the first records for C. g. caudatus in Kenya, describes the distribution of this subspecies, and assesses its conservation status. In September 2014, we found C. g. caudatus in southeast Kenya in Kitobo Forest Reserve (1.6 km2) and Loitokitok Forest Reserve (4.2 km2). This subspecies has an altitudinal range of c. 660–3,050 m asl and an ‘Extent of Occurrence’ of c. 4,040 km2. These findings are important as they: (1) add one subspecies of primate to Kenya’s primate list; (2) remove one endemic subspecies of primate from Tanzania's primate list; (3) establish C. g. caudatus as the most threatened primate subspecies in Kenya; (4) change the priorities for actions necessary to maintain Kenya's primate diversity; and (5) indicate that detailed biodiversity surveys within Kitobo Forest and Loitokitok Forest are likely to yield new data crucial to the conservation of biodiversity in southeast Kenya.
Analysis of relation between placental lesions and perinatal outcome according to Amsterdam criteria: a comparative study

Background: To verify the correlation between histological examination of the placenta (HP), classifying the lesions according to the Amsterdam criteria (AC), and the main neonatal pathological patterns. Methods: This prospective study carried out at the University of Bari between May 2015 and May 2017,enrolled 350 pregnant women. Complete obstetric history and HP was collected. 380 newborns were also enrolled. The analysis was also carried out by comparing the incidence of the various placental pathologies in the sample of physiological pregnancies (PP), represented by 142 cases, with the incidence of the group with placental anomalies (PA). The statistical software used was STATA MP11. Results: Respiratory disorders (61 cases) are significantly correlated with generic PA (p=0.006). Neonatal sepsis (15 cases) was significantly correlated with placental inflammation (p=0.035) and villitis of unknown origin (p=0.039). Twin pregnancies (50 cases) were correlated with generic PA (p=0.00001) and late maternal malperfusion (p=0.00001). Congenital cardiopathies (50 cases) were correlated with the villitis of unknown origin and PA (p=0.0000). Preterm birth (145 cases)was correlated with the premature malperfusion (p=0, 0011) and PA (p=0.0000); SGA (low weight in relation to the gestational age - 75 cases) neonates were correlated with the early malperfusion (p=0.00000) and the generic PA (p=0.00000). Conclusions: The present study has therefore verified whether in reality the HP can be of great help to the neonatologist in the nosological and therapeutic setting of the pathological newborn. The pathological examination of the placenta is nevertheless essential to clarify the causes of the stillbirths and that these causes are particularly important for the obstetric and neonatal outcome of subsequent pregnancies. (www.actabiomedica.it)
Spawning season, maturity sizes, and fecundity in blacktail comber (Serranus atricauda) (Serranidae) from the eastern-central Atlantic

Abstract— Blacktail comber (Ser-ranus atricauda Gunther) is a com-mercially important species in the Canary Islands fisheries. A total of 425 individuals were collected and histological techniques were used to investigate the reproductive data. Results indicated that the spawning season occurred throughout the year, peaking between March and July. Individuals reached 50% maturity at 19.3 cm TL and 95% at 33.1 cm TL. Batch fecundity estimates ranged from 21,774 to 369,578 oocytes per spawning event for specimens from 22.2 to 39.8 cm TL. Blacktail comber was estimated to spawn 42 times/year and 26.5% of individuals spawned, on average, every 3.8 days. Estimates of potential annual fecundity for the species ranged from 0.91 to 15.5 mil-lion oocytes, and an average of 5.1 ±4.1 million. Spawning season, maturity sizes, and fecundity in blacktail comber (Serranus atricauda) (Serranidae) from the eastern-central Atlantic Mercedes Garcia-DiazJose A. Gonzalez
The relationships between nurses' work environments and emotional exhaustion, job satisfaction, and intent to leave among nurses in Saudi Arabia.

AIMS To examine relationships between components of nurses' work environments and emotional exhaustion, job satisfaction and intent to leave among nurses in Saudi Arabia. DESIGN A descriptive correlational study with cross-sectional data. METHODS Data were collected in 2017 from 497 Registered Nurses working in a large tertiary hospital in Riyadh, Saudi Arabia. Participants completed an online survey like that used in RN4Cast studies to measure nurses' perceptions of their work environments and nurse outcomes. Hierarchical linear regression and logistic regression were conducted to examine the relationships between components of nurses' work environments and nurse outcomes after controlling for nurse and patient characteristics. RESULTS Nurse participation in hospital affairs was uniquely associated with all three nurse outcomes, whereas staffing and resource adequacy was associated with emotional exhaustion and job satisfaction, but not intent to leave. These two variables were also the components of the nursing practice environment that received the lowest ratings. Nurse manager ability, leadership and support of nurses, and nurse-physician relationships were associated with job satisfaction only. A nursing foundation for quality of care was not uniquely associated with any of the three outcomes. Finally, nurse emotional exhaustion and job satisfaction fully mediated the relationship between nurse participation in hospital affairs and intent to leave. CONCLUSION Magnet-like work environments in Saudi Arabia are critical to recruiting and retaining nurses in a country with critical nursing shortages. IMPACT This study addresses a gap in the literature regarding which components of the nurses' work environment are uniquely associated with emotional exhaustion, job satisfaction and intent to leave among nurses in Saudi Arabia. Study results will assist Saudi hospital administrators and nurse leaders to develop recruitment and retention strategies by focusing on those work environment components most associated with nurse outcomes: participation in hospital affairs and staffing and resource adequacy.
Correction

GENETICS Correction for “Identification of individuals by trait prediction using whole-genome sequencing data,” by Christoph Lippert, Riccardo Sabatini, M. Cyrus Maher, Eun Yong Kang, Seunghak Lee, Okan Arikan, Alena Harley, Axel Bernal, Peter Garst, Victor Lavrenko, Ken Yocum, Theodore Wong, Mingfu Zhu, Wen-Yun Yang, Chris Chang, Tim Lu, Charlie W. H. Lee, Barry Hicks, Smriti Ramakrishnan, Haibao Tang, Chao Xie, Jason Piper, Suzanne Brewerton, Yaron Turpaz, Amalio Telenti, Rhonda K. Roby, Franz J. Och, and J. Craig Venter, which was first published September 5, 2017; 10.1073/pnas.1711125114 (Proc Natl Acad Sci USA 114:10166–10171). The editors note that the authors had previously provided a conflict of interest statement that was inadvertently omitted during publication. The authors’ statement should have been the following: “Conflict of interest statement: One coauthor, A.T. , disclosed a past collaboration with one of the reviewers, J.-P.H, including PubMed publications PMID 26765343, PMID 25254097,ACMTOPS 10.1145/ 3035538, and conference abstracts in the field of genome privacy. Techniques from their past work are not part of the current publication. The Editorial Board determined that J.-P.H. was acceptable as a reviewer. ”
Celiac disease and headache in children: a narrative state of the art

Celiac disease (CD) is one of the most important entity of the wide spectrum of gluten-related disorders (GRDs). It is well known that neurological manifestation can be present either at the onset of CD, or appear during the development of the pathology, and different can be the neurologic findings. Clinical features are very variable, ranging from typical manifestations of gastrointestinal involvement to neurologic symptom. The most frequent neurologic signs reported were headache, epileptic seizure, migraine, mental retardation, ataxia and attention deficit and hyperactive disorder. Headache either in form of migraine, or in non-specific form represents one of the main clinical presentation in CD. The aim of this work is to provide a narrative review of the pediatric literature focused on the cephalalgic features of children with CD evaluating the potential benefits of a gluten free diet (GFD). Papers were identified by searching for related literature in Medline (PubMed) and Embase using the words “Celiac Disease” and “Headache” or “Migraine” by specifying “children”/“paediatric age” for reports published since 1972 till 31th October 2018. According to our inclusion criteria, a total of 25 papers has been evaluated. Although it is still controversial if headache is prevalent in CD children a correct compliance to a GFD seems to improve the neurological symptoms even if the underlying pathogenic relationship between CD and neurologic system involvement is still not fully understood. (www.actabiomedica.it)
A new species of Pseudotyrannochthonius Beier (Pseudoscorpiones: Pseudotyrannochthoniidae) from the Warrumbungle Range, New South Wales

A new species of the pseudoscorpion genus Pseudotyrannochthonius (family Pseudotyrannochthoniidae) is described from Warrumbungle Range in New South Wales based on morphological features of both males and females. Pseudotyrannochthonius leichhardti sp. nov. is the fourth described species from New South Wales and known only from the type locality. It represents the most inland record of any Pseudotyrannochthonius in Australia.
COVID-19 cases before and after the “I stay at home” decree, Bologna Local Health Authority, Italy

Background and aim of the work: Various measures have been taken by the Italian Government to contain and mitigate the COVID-19 outbreak and on March 11th a decree called “I stay at home” put the whole nation under lockdown. Our aim is to describe sociodemographic and transmission profile of COVID-19 cases that were transmitted before and after the introduction of the decree in the Bologna Local Health Authority. Methods: Cases were classified as transmitted before or after the decree according to the date of last contact with a COVID-19 case or, if this date was unavailable, we used the date of onset of symptoms considering the incubation period. Sociodemographic, clinical and epidemiological information was collected by using the infectious disease monitoring database, hospital discharge, deprivation index and long term care facility databases. Results: In the period after the publication of the decree, there were more elderly, females, strangers, retired, residents in nursing homes and deprived people than in the first period. There were also more health care personnel and less professionals/managers, sales or office workers. In both phases, family is mentioned as the first community attended although less frequently in the second group. Conclusions: The profile of the new COVID-19 cases changed during the outbreak suggesting a differential effect of lockdown measures on the population. An equity lens should be used when analyzing the impact of pandemia and the measures taken to curb it. (www.actabiomedica.it)
Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase

The conserved omega (ω) subunit of RNA polymerase (RNAP) is the only nonessential subunit of bacterial RNAP core. The small ω subunit (7 kDa–11.5 kDa) contains three conserved α helices, and helices α2 and α3 contain five fully conserved amino acids of ω. Four conserved amino acids stabilize the correct folding of the ω subunit and one is located in the vicinity of the β′ subunit of RNAP. Otherwise ω shows high variation between bacterial taxa, and although the main interaction partner of ω is always β′, many interactions are taxon‐specific. ω‐less strains show pleiotropic phenotypes, and based on in vivo and in vitro results, a few roles for the ω subunits have been described. Interactions of the ω subunit with the β′ subunit are important for the RNAP core assembly and integrity. In addition, the ω subunit plays a role in promoter selection, as ω‐less RNAP cores recruit fewer primary σ factors and more alternative σ factors than intact RNAP cores in many species. Furthermore, the promoter selection of an ω‐less RNAP holoenzyme bearing the primary σ factor seems to differ from that of an intact RNAP holoenzyme.
A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations

Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that form two large‐small pairs. We sequenced thousands of ultraconserved elements (UCEs) of the Fiji bush‐warbler Horornis ruficapilla, a passerine distributed on these four Fijian islands, and performed a demographic analysis to test hypotheses of the effects of island size and distance on rates of gene flow. Our demographic analysis inferred low levels of gene flow from each large island to its small counterpart and little or none in the opposite direction. The difference in the distance between these two island pairs manifested itself in lower levels of gene flow between more distant islands. Both findings are generally concordant with classic island biogeography. The amount of reduction in gene flow based on distance was consistent with predictions from island biogeographic equations, while the reduction from small to large islands was possibly greater than expected. These findings offer a hypothesis and framework to guide future study of interisland gene flow in archipelagos as the study of island biogeography progresses into the genomic era.
B Cell Deficiency in Patients with Relapsed and Refractory Acute Myeloid Leukemia

Immune checkpoint inhibition for the treatment of acute myeloid leukemia (AML) has been investigated clinically but has not yet been shown to be more effective than the standard of care treatment [1]. Tumor-specific autologous T cells expressing inhibitory receptors (iRs) are an inherent foundation to this immunotherapy; thus, a detailed picture of cells infiltrating the tumor microenvironment in AML, i.e., the bone marrow (BM), is warranted [2,3]. In this study, we characterized the frequencies and immunophenotypes of adaptive immune cells in the BM of relapsed or refractory AML (R-AML) patients in tandem with age-matched healthy donors (HD) for better contextualization of immunophenotypic variation in both cohorts. We performed deep immunological profiling using multi-parameter flow cytometry of BM of 10 R-AML and 20 age-matched HD, and considered the frequency, composition and expression of clinically relevant iRs across T and B cell subsets in HD and R-AML. Our group previously assessed the BM of this same HD cohort using single-cell RNA sequencing, mass cytometry and flow cytometry to cross-validate these technological approaches and to develop a reference data set for normal immune cell variation in healthy BM [4].