Miracle-dz/UniFAR-FTUs huggingface dataset:
Ticks, Fleas, and Harboured Pathogens from Dogs and Cats in Cyprus

Ticks and fleas are blood-sucking ectoparasites that cause irritation and anaemia to their hosts and act as vectors of pathogens (vector-borne pathogens, VBPs) of relevance for animal and human health. In the present study, tick and flea species in dogs and cats from Cyprus were recorded and VBPs were detected in the collected specimens. Ectoparasites were collected from 220 animals (161 dogs and 59 cats), and a questionnaire including demographic, clinical, and other information was filled out for each animal. The ectoparasites were morphologically identified and the detection of VBPs was performed by PCR-coupled sequencing. Rhipicephalus sanguineus sensu lato was found on 108 dogs and 13 cats, and Ixodes gibbosus on 2 dogs. Ctenocephalides felis was the predominant flea species (on 62 dogs and 45 cats), while one dog and one cat were infested by Ctenocephalides canis and Echidnophaga gallinacea, respectively. The VBPs in ticks were Anaplasma platys, Rickettsia massiliae, Rickettsia conorii, Rickettsia felis, Hepatozoon felis and Hepatozoon canis, while Rickettsia felis, Rickettsia sp. , Bartonella koehlerae, Bartonella clarridgeiae, and Bartonella henselae were recorded in fleas. Statistical analysis (chi-square test and multiple univariate generalized linear model) showed that animals up to 6 months of age were less likely to be infested with ticks than older animals, but more likely to be infested with fleas. Ticks were more prevalent in sheltered than in owned animals, while the odds ratio of flea presence was higher in owned animals than those living in shelters. The present study is the first investigation on the occurrence of ticks and fleas in dogs and cats from Cyprus, showing the presence of different VBPs in these important ectoparasites. The results point out the importance of systematic ectoparasite control in dogs and cats.
Real-world use of antiretroviral therapy and risk of cancer among people with HIV in Texas

Background: Combination antiretroviral therapy (cART) may reduce cancer risk among people with HIV (PWH), but cancer-specific associations are incompletely understood. Methods: We linked HIV and cancer registries in Texas to a national prescription claims database. cART use was quantified as the proportion of days covered (PDC). Cox proportional hazards models assessed associations of cancer risk with cART usage, adjusting for demographic characteristics, AIDS status, and time since HIV report. Results: We evaluated 63 694 PWH followed for 276 804 person-years. The median cART PDC was 21.4% (interquartile range: 0.0–59.8%). cART use was associated with reduced risk of Kaposi sarcoma [adjusted hazard ratio (aHR) 0.48, 95% confidence interval (CI) 0.34–0.68 relative to unexposed status] and non-Hodgkin lymphoma (aHR 0.41, 95% CI 0.31–0.53), liver cancer (aHR 0.61, 95% CI 0.39–0.96), anal cancer (aHR 0.65, 95% CI 0.46–0.92), and a miscellaneous group of ‘other’ cancers (aHR 0.80, 95% CI 0.66–0.98). In contrast, cART-exposed status was not associated with risk for cervical, lung, colorectal, prostate or breast cancers. Conclusion: In a large HIV cohort incorporating data from prescription claims, cART was associated with greatly reduced risks of Kaposi sarcoma and non-Hodgkin lymphoma, and to a lesser degree, reduced risks of liver and anal cancers. These associations likely reflect the beneficial effects of HIV suppression and improved immune control of oncogenic viruses. Efforts to increase cART use and adherence may further decrease cancer incidence among PWH.
The sociodemographic patterning of sick leave and determinants of longer sick leave after mild and severe COVID-19: a nationwide register-based study in Sweden

Abstract Background Studies on sociodemographic differences in sick leave after coronavirus disease 2019 (COVID-19) are limited and research on COVID-19 long-term health consequences has mainly addressed hospitalized individuals. The aim of this study was to investigate the social patterning of sick leave and determinants of longer sick leave after COVID-19 among mild and severe cases. Methods The study population, from the Swedish multi-register observational study SCIFI-PEARL, included individuals aged 18–64 years in the Swedish population, gainfully employed, with a first positive polymerase chain reaction (PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from 1 January 2020 until 31 August 2021 (n = 661 780). Using logistic regression models, analyses were adjusted for sociodemographic factors, vaccination, prior sick leave, comorbidities and stratified by hospitalization. Results In total, 37 420 (5.7%) individuals were on sick leave due to COVID-19 in connection with their first positive COVID-19 test. Individuals on sick leave were more often women, older, had lower income and/or were born outside Sweden. These differences were similar across COVID-19 pandemic phases. The highest proportion of sick leave was seen in the oldest age group (10.3%) with an odds ratio of 4.32 (95% confidence interval 4.18–4.47) compared with the youngest individuals. Among individuals hospitalized due to COVID-19, the sociodemographic pattern was less pronounced, and in some models, even reversed. The intersectional analysis revealed considerable variability in sick leave between sociodemographic groups (range: 1.5–17.0%). Conclusion In the entire Swedish population of gainfully employed individuals, our findings demonstrated evident sociodemographic differences in sick leave due to COVID-19. In the hospitalized group, the social patterning was different and less pronounced.
TOXOPLASMA GONDII DOES NOT INHIBIT THE ASSISTED COLONIZATION OF EASTERN BARRED BANDICOOTS (PERAMELES GUNNII) TO PHILLIP ISLAND, VICTORIA, AUSTRALIA

Abstract: Eastern barred bandicoots (Perameles gunnii) are thought to be highly susceptible to disease caused by infection with the protozoan parasite Toxoplasma gondii. This study followed a population of 67 P. gunnii introduced onto the Summerland Peninsula, Phillip Island, Australia, where the prevalence of T. gondii infection in the feral cat population was known to be very high. Prior to release, bandicoots were tested for serologic exposure to T. gondii using the modified agglutination test. A subset of bandicoots was tested on four occasions after release onto the peninsula. No seroconversion was detected at any time point. A subset of bandicoots was radiotracked after release and at two additional trapping sessions to help monitor survival. Toxoplasma gondii DNA was not detected by PCR in eight carcasses recovered for necropsy. Fourteen founder bandicoots (21% of founders) were known to be alive at 500 d post-release. A total of 29 unmarked bandicoots were trapped over the study period, confirming that the bandicoots were successfully reproducing on the island. Body weight, packed cell volume, and total plasma protein were used as measures of individual animal health; population health was inferred from these data. Body weight was significantly associated with trip number, with a general trend of increasing weight after release onto the island. This study showed that eastern barred bandicoots were able to establish a new population despite a probably high environmental load of T. gondii.
Reliability of systolic blood pressure measured by parents in young children at home using a hand held doppler device and aneroid sphygmomanometer

Objective: We report data regarding systolic BP monitoring in children aged <5 years performed over a 2-week period by parents at home using a hand-held doppler device and aneroid sphygmomanometer for SBP measurements (HDBPM). Our objectives were to compare health professional measured office systolic BP by doppler device (Office-SBPDoppler) with parent measured home systolic BP using the same doppler device (Home-SBPDoppler). We also report data evaluating reliability and optimal number of days of measurement required. Design and Methods: We taught parents to measure systolic BP and assessed their technique using a hand-held doppler device and aneroid sphygmomanometer. We requested parents to perform three consecutive BP measurements twice daily (ideally morning and evening around similar times) when the child was awake, settled and cooperative. Results: Over a 3-year period, data from 48 of 62 children who underwent HDBPM measurements were evaluated with median (IQR) age of 1.9 (0.9, 3.6) years, 27 (56%) boys and 14 (29%) on antihypertensive medication. Office-SBPDoppler was 2.9 ± 8.9 mmHg [95% confidence interval (CI), −14.4 to 20.4, P = 0.026] higher than Home-SBPDoppler. Mean Home-SBPDoppler between Week-1 and Week-2 monitoring was similar −0.45 ± 3.5 mmHg (95% CI, −7.35 to 6.45, P = 0.41). Morning HDBPM measurements were lower than evening with a mean difference of -2.77 ± 3.92 mmHg, P < 0.001). Over Week-1, mean Home-SBPDoppler was closer to mean Office-SBPDoppler with increasing cumulative days of monitoring and with smaller standard deviations suggesting that readings become more reliable from day 4 onwards. Conclusions: HDBPM is a reliable method for measuring systolic BP in young children with BP levels measured by parents comparable to those performed by health professional in clinic. HDBPM technique described here and performed by parents over a 7-day period with a minimum of 4-days, offers a reliable and reproducible technique to measure blood pressure at home.
Impact of Specialized Treatment Setting on Survival in Adolescent and Young Adult ALL

PURPOSE Unlike children with ALL who receive cancer care primarily at specialized cancer centers (SCCs; National Cancer Institute and/or Children's Oncology Group centers), adolescents and young adults (AYAs; 15-39 years) receive care in a variety of settings. Using population-based data, we describe where AYAs with ALL receive treatment and determine associations with overall survival (OS). METHODS Data from the 2004 to 2018 California (CA, n = 2,283), New York (NY, n = 795), and Texas (TX, n = 955) state cancer registries were used to identify treatment setting of AYAs with newly diagnosed ALL. Multivariable Cox proportional hazards regression models evaluated associations with OS. RESULTS Seventy percent were older than 18 years, and 65% were male. A majority in CA (63%) and TX (64%) were Hispanic while most in NY were non-Hispanic White (50%). Treatment at an SCC occurred in 48.2% (CA), 44.4% (NY), and 19.5% (TX). Across states, AYAs who were older or uninsured were less likely to receive treatment at an SCC. Treatment at an SCC was associated with superior OS in CA (hazard ratio [HR], 0.73; 95% CI, 0.63 to 0.85) and TX (HR, 0.61; 95% CI, 0.45 to 0.83); a nonsignificant association was seen in NY (HR, 0.83; 95% CI, 0.64 to 1.08). CONCLUSION Only 20%-50% of AYA patients with ALL received frontline treatment at SCCs. Treatment of ALL at an SCC was associated with superior survival, highlighting the importance of policy efforts to improve access and reduce inequities in AYA ALL care.
Automated Cough Sound Analysis for Detecting Childhood Pneumonia

Pneumonia is one of the leading causes of death in children. Prompt diagnosis and treatment can help prevent these deaths, particularly in resource poor regions where deaths due to pneumonia are highest. Clinical symptom-based screening of childhood pneumonia yields excessive false positives, highlighting the necessity for additional rapid diagnostic tests. Cough is a prevalent symptom of acute respiratory illnesses and the sound of a cough can indicate the underlying pathological changes resulting from respiratory infections. In this study, we propose a fully automated approach to evaluate cough sounds to distinguish pneumonia from other acute respiratory diseases in children. The proposed method involves cough sound denoising, cough sound segmentation, and cough sound classification. The denoising algorithm utilizes multi-conditional spectral mapping with a multilayer perceptron network while the segmentation algorithm detects cough sounds directly from the denoised audio waveform. From the segmented cough signal, we extract various handcrafted features and feature embeddings from a pretrained deep learning network. A multilayer perceptron is trained on the combined feature set for detecting pneumonia. The method we propose is evaluated using a dataset comprising cough sounds from 173 children diagnosed with either pneumonia or other acute respiratory diseases. On average, the denoising algorithm improved the signal-to-noise ratio by 44%. Furthermore, a sensitivity and specificity of 91% and 86%, respectively, is achieved in cough segmentation and 82% and 71%, respectively, in detecting childhood pneumonia using cough sounds alone. This demonstrates its potential as a rapid diagnostic tool, such as using smartphone technology.
Establishment of organoid models for pancreatic ductal adenocarcinoma and screening of individualized therapy strategy

Patients with pancreatic ductal adenocarcinoma (PDAC) who undergo surgical resection and receive effective chemotherapy have the best chance for long‐term survival. Unfortunately, because of the heterogeneity of pancreatic cancer, it is difficult to find a personalized treatment strategy for patients. Organoids are ideal preclinical models for personalized medicine. Therefore, we explore the cultivation conditions and construction methods of PDAC organoid models to screen the individualized therapy strategy.
Diverse gut pathogens exploit the host engulfment pathway via a conserved mechanism

Macrophages clear infections by engulfing and digesting pathogens within phagolysosomes. Pathogens escape this fate by engaging in a molecular arms race; they use WxxxE motif-containing “effector” proteins to subvert the host cells they invade and seek refuge within protective vacuoles. Here we define the host component of the molecular arms race as an evolutionarily conserved polar ‘hotspot’ on the PH-domain of ELMO1 (Engulfment and Cell Motility1), which is targeted by diverse WxxxE-effectors. Using homology modeling and site-directed mutagenesis, we show that a lysine triad within the ‘patch’ directly binds all WxxxE-effectors tested: SifA (Salmonella), IpgB1 and IpgB2 (Shigella), and Map (enteropathogenic E. coli). Using an integrated SifA•host protein-protein interaction (PPI) network, in-silico network perturbation, and functional studies we show that the major consequences of preventing SifA•ELMO1 interaction are reduced Rac1 activity and microbial invasion. That multiple effectors of diverse structure, function, and sequence bind the same hotpot on ELMO1 suggests that the WxxxE-effector(s)•ELMO1 interface is a convergence point of intrusion detection and/or host vulnerability. We conclude that the interface may represent the fault line in co-evolved molecular adaptations between pathogens and the host and its disruption may serve as a therapeutic strategy. GRAPHICAL ABSTRACT In brief: This work defines the nature of a conserved molecular interface, assembled between diverse WxxxE motif-containing effector proteins encoded by gut pathogens and the host innate immune sensor, ELMO1, via which pathogens exploit the host’s engulfment machinery.
White matter integrity and its association with amyloid-PET and serum NfL in healthy APOE4 homozygotes, heterozygotes and non-carries

Except for aging, APOE epsilon4 allele (APOE4) is the most important risk factor for sporadic Alzheimer's disease. APOE4 carriers may have reduced capacity to recycle lipids, resulting in reduced white matter integrity. Here, we evaluated if white matter impairment measured by diffusion tensor imaging (DTI) differs between healthy individuals with different number of APOE4 alleles and if white matter impairment associates with brain beta-amyloid (Ab) load and serum levels of neurofilament light chain (NfL). We studied 96 participants (APOE4/4, N = 20; APOE4/3, N = 39; APOE3/3, N = 37; mean age 70.7 (SD 5.22) years, 63% females) with brain MRI including a DTI sequence (N = 96), Ab-PET (N = 89) and a venous blood sample for serum NfL concentration measurement (N = 88). Fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD) and axial diffusivity (AxD) in six a priori-selected white matter regions-of-interest (ROIs) were compared between the groups using ANCOVA, with sex and age as covariates. A voxel-weighted average of FA, MD, RD and AxD was calculated for each subject, and correlations with Ab-PET and NfL levels were evaluated. APOE4/4 carriers exhibited higher MD and higher RD in the body of corpus callosum than APOE4/3 (p = 0.0053 and p = 0.0049, respectively) and APOE3/3 (p = 0.026 and p = 0.042). APOE4/4 carriers had higher AxD than APOE4/3 (p = 0.012) and APOE3/3 (p = 0.040) in the right cingulum adjacent to cingulate cortex. In the total sample, composite MD, RD and AxD positively correlated with cortical Ab load (r = 0.26 to 0.33, p < 0.013 for all) and with serum NfL concentrations (r = 0.31 to 0.36, p < 0.0028 for all). In conclusion, reduced white matter integrity was detected in cognitively unimpaired APOE4/4 homozygotes compared to APOE4/3 and APOE3/3 carriers and reduced white matter integrity correlated with biomarkers of Alzheimer's disease and neurodegeneration. White matter impairment seems to be an early phenomenon in the Alzheimer's disease pathologic process in APOE4/4 homozygotes.
Gastric inhibitory polypeptide receptor antagonism suppresses intramuscular adipose tissue accumulation and ameliorates sarcopenia

Intramuscular adipose tissue (IMAT) formation derived from muscle fibro‐adipogenic progenitors (FAPs) has been recognized as a pathological feature of sarcopenia. This study aimed to explore whether genetic and pharmacological gastric inhibitory polypeptide (GIP) receptor antagonism suppresses IMAT accumulation and ameliorates sarcopenia in mice.
Surface-sediment composition and sedimentary processes in the central Arctic Ocean and along the Eurasian Continental Margin

The extent of the Arctic sea-ice cover ranges between 9.3 X 106 km2 in summer and 15.7 X 1 o6 km2 in winter. It controls the exchange between ocean and atmosphere and is of global climatic importance. The mediterranean character of the Arctic Ocean results in the formation of a multi-year ice cover, on average between 3 and 5 m thick. Circulation within the Arctic Basin is mostly wind-driven, with two major circulation Systems, the Beaufort Gyre and the Transpolar Drift. Over the American and Eurasian shelves sea ice may entrain significant amounts of particulate matter, which is exported with the ice into the Arctic Basin, eventually released upon ice melting in the European Nordic Seas. Thus, an understanding of the present-day and past patterns of surface sediment distributions requires a thorough knowledge of sea-ice dynamics. Based on a review of the available literature and studies with a large-scale dynamic-thermodynamic sea-ice model, the general drift patterns and their variability as well as their geological relevance are discussed.
Genome-Wide Identiﬁcation and Expression Analysis of Lipoxygenase Genes in Rose ( Rosa chinensis )

: Lipoxygenases (LOX) play pivotal roles in plant resistance to stresses. However, no study has been conducted on LOX gene identiﬁcation at the whole genome scale in rose ( Rosa chinensis ). In this study, a total of 17 RcLOX members were identiﬁed in the rose genome. The members could be classiﬁed into three groups: 9-LOX, Type I 13-LOX, and Type II 13-LOX. Similar gene structures and protein domains can be found in RcLOX members. The RcLOX genes were spread among all seven chromosomes, with unbalanced distributions, and several tandem and proximal duplication events were found among RcLOX members. Expressions of the RcLOX genes were tissue-speciﬁc, while every RcLOX gene could be detected in at least one tissue. The expression levels of most RcLOX genes could be up-regulated by aphid infestation, suggesting potential roles in aphid resistance. Our study offers a systematic analysis of the RcLOX genes in rose, providing useful information not only for further gene cloning and functional exploration but also for the study of aphid resistance.
Genome-Wide Identiﬁcation and Expression Analysis of BnPP2C Gene Family in Response to Multiple Stresses in Ramie ( Boehmeria nivea L.)

: The protein phosphatase 2C ( PP2C ), a key regulator of the ABA signaling pathway, plays important roles in plant growth and development, hormone signaling, and abiotic stress response. Although the PP2C gene family has been identiﬁed in many species, systematic analysis was still relatively lacking in ramie ( Boehmeria nivea L.). In the present study, we identiﬁed 63 BnPP2C genes from the ramie genome, using bioinformatics analysis, and classiﬁed them into 12 subfamilies, and this classiﬁcation was consistently supported by their gene structures and conserved motifs. In addition, we observed that the functional differentiation of the BnPP2C family of genes was restricted and that fragment replication played a major role in the ampliﬁcation of the BnPP2C gene family. The promoter cis -regulatory elements of BnPP2C genes were mainly involved in light response regulation, phytohormone synthesis, transport and signaling, environmental stress response and plant growth and development regulation. We identiﬁed BnPP2C genes with tissue speciﬁcity, using ramie transcriptome data from different tissues, in rhizome leaves and bast ﬁbers. The qRT-PCR results showed that the BnPP2C1 , BnPP2C26 and BnPP2C27 genes had a strong response to drought, high salt and ABA, and there were a large number of stress-responsive elements in the promoter region of BnPP2C1 and BnPP2C26 . The results suggested that BnPP2C1 and BnPP2C26 could be used as the candidate genes for drought and salt tolerance in ramie. These results provide a reference for further studies on the function of the PP2C gene and advance the development of the mechanism of ramie stress response, with a view to providing candidate genes for the molecular breeding of ramie for drought and salt tolerance.
Identiﬁcation and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots

: Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was signiﬁcantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modiﬁcations of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m 6 A), it was found that the enrichment of histone modiﬁcations associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These ﬁndings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.