Miracle-dz/UniFAR-FTUs huggingface dataset:
Chronic chlamydial infection: impact on human reproductive health : reproductive health research in the Northern Finland 1966 Birth Cohort (NFBC 1966)

Chlamydiae are obligatory intracellular gram-negative bacteria with a unique growth cycle. They are very successful pathogens and responsible for a wide variety infections in humans and different animal species. In addition, they have a tendency to cause recurrent, persistent or chronic infections with potentially severe sequelae years or decades later. The general purpose of this work was to study the possible serological associations between chronic chlamydial infection, systemic inflammation and reproductive health in a general population. The chlamydial heat shock proteins 60 and 10 (Hs10 and Hsp60) have been suggested to contribute to the pathogenesis of chronic chlamydial infections. Thus, the antibodies to chlamydial Hsp10 and Hsp60 were also investigated in complications of pregnancy. The present study was a longitudinal population-based birth cohort study, and all of the original papers of this dissertation are based on a nested case control design. Our results confirmed the serological association between C. trachomatis infections and subfertility and the rather high incidence of undiagnosed C. trachomatis infections in the male partners of subfertile couples. We further demonstrated a serological association between previous C. trachomatis infections, immunity to chlamydial Hsps and female subfertility. We also showed that serological markers of chronic chlamydial infection present as early as the first trimester are associated with preterm delivery among nulliparous women. When elevated levels of C. trachomatis IgG and hsCRP were present, the estimated risk for preterm delivery was over 4-fold. According to our study, nulliparous women who subsequently developed preeclampsia leading to preterm delivery, which was used as a marker of more serious illness, had significantly more often serum IgG antibodies to C. pneumoniae during the first trimester of pregnancy compared to the preeclamptic women who delivered at term. In conclusion, chronic C. trachomatis infection was found to associate with subfertility both in men and in women. In addition, a subclinical chronic inflammatory process associated at least partly with chronic C. trachomatis infection and present in the first trimester already may be important in the development of preterm delivery. Chronic C. pneumoniae infection and systemic low-grade inflammation were found to associate with pregnancies that lead to preeclampsia and preterm delivery.
Biosecurity Threat Posed by Botulinum Toxin

The deliberate release of biological agents with terrorist or criminal intent continues to pose concerns in the current geopolitical situation. Therefore, attention is still needed to ensure preparedness against the potential use of pathogens as unconventional weapons. Botulinum neurotoxin (BoNT) is one such biological threat, characterized by an extremely low lethal dose, high morbidity and mortality when appropriately disseminated, and the capacity to cause panic and social disruption. This paper addresses the risks of a potential release of the botulinum neurotoxin and summarizes the relevant aspects of the threat.
Epstein‐Barr virus infections are strongly dependent on activating and inhibitory KIR‐HLA pairs after T‐cell replate unrelated hematopoietic stem cell transplantation, the principles, and method of pairing analysis

Viral infections are the main cause of increased morbidity and mortality among recipients in allogeneic hematopoietic stem cell transplantation (HSCT). Natural killer (NK) cells fight virally infected cells provided directional activation of cytotoxicity. In this study, we analyzed the role of receptor‐ligand pairs that include inhibitory or activating killer cell immunoglobulin‐like receptors (KIRs) with their HLA class I ligands in the course of viral infections. The paper also presents an algorithm that allows performing automated inhibitory (i) KIR:HLA pairing and rechecking in the clinical setting. The obtained results indicate a significant adverse roles of reduced number of iKIR:HLA pairs (40% vs 9%; odds ratio [OR] = 6.67; P = .0057; 95% confidence interval [CI] 1.74‐25.62) and the presence of activating KIR:HLA pairs (15% vs 5%, OR = 3.58, P = .028, 95% CI 1.19‐10.73) in EBV infections post HSCT.
PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection

Cohesin is a chromatin-bound complex that mediates sister chromatid cohesion and facilitates long-range interactions through DNA looping. How the transcription and replication machineries deal with the presence of cohesin on chromatin remains unclear. The dynamic association of cohesin with chromatin depends on WAPL cohesin release factor (WAPL) and on PDS5 cohesin-associated factor (PDS5), which exists in two versions in vertebrate cells, PDS5A and PDS5B. Using genetic deletion in mouse embryo fibroblasts and a combination of CRISPR-mediated gene editing and RNAi-mediated gene silencing in human cells, here we analyzed the consequences of PDS5 depletion for DNA replication. We found that either PDS5A or PDS5B is sufficient for proper cohesin dynamics and that their simultaneous removal increases cohesin's residence time on chromatin and slows down DNA replication. A similar phenotype was observed in WAPL-depleted cells. Cohesin down-regulation restored normal replication fork rates in PDS5-deficient cells, suggesting that chromatin-bound cohesin hinders the advance of the replisome. We further show that PDS5 proteins are required to recruit WRN helicase-interacting protein 1 (WRNIP1), RAD51 recombinase (RAD51), and BRCA2 DNA repair associated (BRCA2) to stalled forks and that in their absence, nascent DNA strands at unprotected forks are degraded by MRE11 homolog double-strand break repair nuclease (MRE11). These findings indicate that PDS5 proteins participate in replication fork protection and also provide insights into how cohesin and its regulators contribute to the response to replication stress, a common feature of cancer cells.
Contact evaluation and isoniazid preventive therapy among close and household contacts of tuberculosis patients in Lima, Peru: an analysis of routine data

Contacts of pulmonary tuberculosis (TB) cases are at high risk of TB infection and progression to disease. Close and household contacts and those <5 years old have the highest risk. Isoniazid preventive therapy (IPT) can largely prevent TB disease among infected individuals. International and Peruvian recommendations include TB contact investigation and IPT prescription to eligible contacts. We conducted a study in Lima, Peru, to determine the number of close and household contacts who were evaluated, started on IPT, and who completed it, and the factors associated to compliance with national guidelines.
Immune dysregulation increases the incidence of delayed‐type drug hypersensitivity reactions

Delayed‐type, T cell–mediated, drug hypersensitivity reactions are a serious unwanted manifestation of drug exposure that develops in a small percentage of the human population. Drugs and drug metabolites are known to interact directly and indirectly (through irreversible protein binding and processing to the derived adducts) with HLA proteins that present the drug‐peptide complex to T cells. Multiple forms of drug hypersensitivity are strongly linked to expression of a single HLA allele, and there is increasing evidence that drugs and peptides interact selectively with the protein encoded by the HLA allele. Despite this, many individuals expressing HLA risk alleles do not develop hypersensitivity when exposed to culprit drugs suggesting a nonlinear, multifactorial relationship in which HLA risk alleles are one factor. This has prompted a search for additional susceptibility factors. Herein, we argue that immune regulatory pathways are one key determinant of susceptibility. As expression and activity of these pathways are influenced by disease, environmental and patient factors, it is currently impossible to predict whether drug exposure will result in a health benefit, hypersensitivity or both. Thus, a concerted effort is required to investigate how immune dysregulation influences susceptibility towards drug hypersensitivity.
Acceptability of a digital patient notification and linkage-to-care tool for French PrEPers (WeFLASH©): Key stakeholders' perspectives

The objective of this study was to describe stakeholders’ perspectives on the acceptability of WeFLASH© (AADISS, Paris, France), a digital smartphone sexually transmitted infection (STI) patient notification (PN) tool to be launched among French HIV pre-exposure prophylaxis users (PrEPers). In Paris, Lyon, and Nice, we conducted 2-hour focus group discussions with PrEPers (n = 21) and community mediators (n = 10), and one-on-one interviews with PrEP-prescribing physicians (n = 5) and HIV/STI management decision-makers (n = 4). Recordings were transcribed. The analysis focused on perceived benefits and risks. Concerning benefits, participants mentioned that WeFLASH© could provide: improved PN and STI screening, by refining the notification of anonymous partners; customized linkage-to-care, by providing users with tailored information on care; and transferable epidemiological data, by filling a need for real-time data. Participants anticipated risks for: privacy and confidentiality and suggested specific security settings to protect users’ identity; sexual behavior and suggested game-like functions to improve the integration of the tool in sexual contexts; and fairness and emphasized the importance of making WeFLASH© accessible to all men who have sex with men. WeFLASH© could facilitate PN for an increasing proportion of anonymous partners met online, and empower users, including notified partners, on questions of confidentiality and consent, access to STI prevention and screening services, and access to data.
Profile of stroke-related late onset epilepsy among Nigerians

Background: Cerebrovascular diseases have become an increasingly common cause of seizure in the later years of life in the developing countries. Despite the huge data from the developed world on the subject matter, there is paucity of information on this from Nigeria. Methodology: In a study of late onset epilepsy (i.e onset of epilepsy at =25 yrs.) in which a total of 302 consecutive patients were recruited. in three tertiary centres from northern and southern Nigeria, those with neuroimaging finding in keeping with stroke were selected to to determine their clinical , neuroimaging and electroencephalographic profile as well as response to anticonvulsants. Result: Sixty eight (39 males, 29 females) out of 302 (22.5%) patients with late onset epilepsy (LOE) were studied. Their ages ranged between 39 and 77 years (SD=10). 58 subjects had cerebral infarction while10 were hemorrhagic. 53 of the 58 patients with infarction involved the cerebral cortex. The most common seizure type was simple partial diagnosed in forty eight (70.6%) subjects. Electroencephalography (EEG) was abnormal in 46 (67.6%) of the patients. The most common EEG finding was the presence of focal epileptiform discharges (47.1%) followed by focal slowing (8.8%). At 3-month follow up, 52% of the patients had good seizure control. Our results highlight demographic, EEG and clinical pattern of post-stroke epilepsy, importance of neuroimaging LOE is emphasized. Key Words : Epilepsy, late onset profile
Cell Biology International

Squamous cell carcinoma (SCC) of the tongue is associated with tobacco use, alcohol abuse, and human papillomavirus (HPV) infections. While clinical outcomes have recently improved for HPV‐positive patients in general, 50% of patients suffering from tongue cancer die within 5 years of being diagnosed. Flavonoids are secondary plant metabolites with a wide range of biological activities including antioxidant, anti‐inflammatory, and anticancer activities. Flavonoids have generated high interest as therapeutic agents owing to their low toxicity and their effects on a large variety of cancer cell types. In this literature review, we evaluate the actions of flavonoids on SCC of the tongue demonstrated in both in vivo and in vitro models.
Influenza A virus-induced host caspase and viral PA-X antagonize the antiviral host factor, histone deacetylase 4

Influenza A virus (IAV) effectively manipulates host machinery to replicate. There is a growing evidence that an optimal acetylation environment in the host cell is favorable to IAV proliferation and vice versa. The histone deacetylases (HDACs), a family of 18 host enzymes classified into four classes, are central to negatively regulating the acetylation level, hence the HDACs would not be favorable to IAV. Indeed, by using the RNAi and overexpression strategies, we found that human HDAC4, a class II member, possesses anti-IAV properties and is a component of host innate antiviral response. We discovered that IAV multiplication was augmented in HDAC4-depleted cells and abated in HDAC4-supplemented cells. Likewise, the expression of IFITM3, ISG15, and viperin, some of the critical markers of host anti-IAV response was abated in HDAC4-depleted cells and augmented in HDAC4-supplemented cells. In turn, IAV strongly antagonizes the HDAC4, by down-regulating its expression both at the mRNA level via viral RNA endonuclease PA-X and at the polypeptide level by inducing its cleavage via host caspase 3 in infected cells. Such HDAC4 polypeptide cleavage resulted in a ∼30 kDa fragment that is also observed in some heterologous systems and may have a significant role in IAV replication.
Sequencing and Extent of Integration in Asia: The Real Financial Dimensions

This paper examines some of the salient issues surrounding the degree of economic integration among Asian countries with particular attention being paid to the nexus between real and financial integration. Using a novel and simple method, we derive some measures of price-based real and financial integration from the relative PPP and UIP relation. We then investigate the degree of integration between countries and groups of countries and analyze the sequence of integration – the extent to which the existence of one might cause the other. We find that, overall, integration is generally higher after the Asian crisis but the results are quite close. The original ASEAN nations – Indonesia, Malaysia, the Philippines, Singapore and Thailand – seem to be more integrated with rest of Asia than are other groups. The results of the dynamic estimations suggest that financial integration might lead real integration but not necessarily the opposite. This result may reflect the difference in the timing of adjustment of the respective markets. The paper concludes with some pertinent policy implications for the region.
Analytical solution for a hybrid Logistic‐Monod cell growth model in batch and continuous stirred tank reactor culture

Abstract Monod and Logistic growth models have been widely used as basic equations to describe cell growth in bioprocess engineering. In the case of the Monod equation, the specific growth rate is governed by a limiting nutrient, with the mathematical form similar to the Michaelis–Menten equation. In the case of the Logistic equation, the specific growth rate is determined by the carrying capacity of the system, which could be growth‐inhibiting factors (i.e., toxic chemical accumulation) other than the nutrient level. Both equations have been found valuable to guide us build unstructured kinetic models to analyze the fermentation process and understand cell physiology. In this work, we present a hybrid Logistic‐Monod growth model, which accounts for multiple growth‐dependent factors including both the limiting nutrient and the carrying capacity of the system. Coupled with substrate consumption and yield coefficient, we present the analytical solutions for this hybrid Logistic‐Monod model in both batch and continuous stirred tank reactor (CSTR) culture. Under high biomass yield (Y x/s) conditions, the analytical solution for this hybrid model is approaching to the Logistic equation; under low biomass yield condition, the analytical solution for this hybrid model converges to the Monod equation. This hybrid Logistic‐Monod equation represents the cell growth transition from substrate‐limiting condition to growth‐inhibiting condition, which could be adopted to accurately describe the multi‐phases of cell growth and may facilitate kinetic model construction, bioprocess optimization, and scale‐up in industrial biotechnology.
Serological and Molecular Identification of Brucella spp. in Pigs from Cairo and Giza Governorates, Egypt

Brucellosis is considered as endemic disease of animals and humans since thousands of years in Egypt. However, brucellosis in pigs has never been reported in Egypt. Thus, serological and molecular assays were applied to detect anti-Brucella antibodies and DNA in serum samples collected from pigs. In total 331 blood samples collected from male and female pigs at slaughterhouses of Cairo and Giza governorates were investigated using Brucella c- and i-ELISA and Brucella real-time PCR. Anti-Brucella antibodies were detected in 16 (4.83%) and 36 (10.8%) sera by i-ELISA and c-ELISA, respectively. Brucella DNA was detected in 10 (3.02%) seropositive samples and identified as Brucella melitensis (7/10) and Brucella suis (3/10). A higher prevelance was found in boars. This is the first study investigating pig brucellosis in Egypt. The results of this study will raise awareness for brucellosis in these farm animals and will help to develop effective control strategies.
The gene encoding ganglioside- induced differentiation-associated protein 1 is mutated in axonal Charcot-Marie-Tooth type 4A disease

frequently occurring inherited peripheral neuropathy. CMT is classified in two main groups1,2: (i) demyelinating CMT, associated with reduced nerve conduction velocities and segmental deand remyelination and onion bulb formations, and (ii) axonal CMT, characterized by axonal degeneration without demyelinating lesions and the presence of clusters of regeneration. We diagnosed an axonal CMT phenotype associated with hoarse voice and vocal cord paresis in two small families, LF20 and LF249, and one large inbred family, LF38, with Spanish ancestry. The disease segregates as an autosomal recessive trait. The clinical picture is characterized by onset at childhood with weakness and foot and hand wasting, leading to disability at the end of the first decade3. Sensory-nerve action potentials were decreased or absent in all affected individuals. In families LF20 and LF249, we did not register median, ulnar, and peroneal compound motor action potentials (CMAPs). However, we obtained The gene encoding gangliosideinduced differentiation-associated protein 1 is mutated in axonal Charcot-Marie-Tooth type 4A disease
Phenotypes for novel functional traits of dairy cattle

Modern dairying uses sophisticated data collection systems to maximize farm profitability. This includes information on cows and their environments. As on-farm automation increases many more phenotypes can be collected. There are two principal sources of data: farms and laboratories. On-farm data typically are recorded by farmers, but it is now common for information to be collected by other experts. For example, claw health data often are recorded by hoof trimmers. Automated milking systems provide detailed information about individual milkings, including time and conductivity for mastitis detection, and tools exist to assay progesterone in real-time. However, those systems often integrate poorly with the software used to interface with milk recording programs. Some farms have automated stations to record climate data, but much environmental information is not captured in on-farm systems, e.g., housing and flooring types and ration composition. Many phenotypes are based on the laboratory analysis of milk samples, and spectroscopic analysis is used to determine milk and fat concentrations in milk. Recent research suggests that many other phenotypes can be collected from those data, including milk fatty acid composition and methane production. The latter trait may provide a more economical measure of feed efficiency than individual intakes. There are also milk ELISAbased tests for diseases such as paratuberculosis and leucosis to provide early identification of carriers. Many young animals are genotyped, but only summary data are stored on the farm. Some phenotypes, most notably haplotypes associated with reduced fertility and increased perinatal mortality, can be generated directly from data collected in national databases. There are now more than a dozen of these recessives tracked in the US and other countries. The most substantial challenge faced by many dairy managers will be the effective use of the many new phenotypes that now are available.
Variability in Operative Management of Proximal Humerus Fractures

Background Controversy exists regarding the best methods for the operative management of proximal humerus fractures. We hypothesized that trauma surgeons perform the majority of these procedures and that there is variability in the type of fixation used at our institutions based on the type of fellowship training. Methods A retrospective review of 177 consecutive operative closed proximal humerus fractures was conducted. All images were classified based on the Neer system, including: simple (two-part surgical neck or isolated tuberosity) or complex (three- or four-part). Choice of fixation was determined based on surgeon subspecialty. Results One-hundred and nine procedures were performed by trauma, 45 by shoulder, and 17 by hand. Thirty-eight percent (67/177) were simple and 62% (110/177) were complex. A significant difference was only found in blade plating of two-part surgical neck fractures (p < 0.05) and the management of tuberosity fractures (p < 0.05). Analysis of complex fractures showed a significant difference in the rate of arthroplasty (p < 0.05). Discussion Trauma surgeons perform the majority of procedures on proximal humerus fractures, although at a similar rate to shoulder surgeons. A significant difference in management was found with regard to the utilization of blade plating, arthroplasty and the management of tuberosity fractures.
Heart failure in the elderly

Heart failure (HF) is a major clinical and public health problem. It refers to approximately 1-2% of the adult population of developed countries, and the prevalence of HF increases with advanced age. The signs and symptoms of HF can be non-specific and they are often the results of pathophysiological changes that occur at the aging process. Until now, the clear criteria that allowed to diagnose HF have not been developed. The diagnosis of HF is usually based on combined assessment of clinical and chest X-ray examinations, electrocardiography, transthoracic echocardiography as well as serum B-type natriuretic peptide (BNP) and N-terminal pro-BNP (NT-pro-BNP) concentrations. The proper medical attendance in patients with HF, apart from pharmacological treatment, should contain non-pharmacological procedures such as supervised physical activity, modification of the lifestyle, low-sodium diet, alcohol restriction and weight control. Particularly intensive therapy should be employed in overweight or obese patients with hypertension, dyslipidemia and diabetes because of significantly increased risk of development and rapid progression of symptoms of HF.