Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling within-host macrophage dynamics in influenza virus infection

Human respiratory disease associated with influenza virus infection is of significant public health concern. Macrophages, as part of the front line of host innate cellular defence, have been shown to play an important role in controlling viral replication. However, fatal outcomes of infection, as evidenced in patients infected with highly pathogenic viral strains, are often associated with prompt activation and excessive accumulation of macrophages. Activated macrophages can produce a large amount of pro-inflammatory cytokines, which leads to severe symptoms and at times death. However, the mechanism for rapid activation and excessive accumulation of macrophages during infection remains unclear. It has been suggested that the phenomena may arise from complex interactions between macrophages and influenza virus. In this work, we develop a novel mathematical model to study the relationship between the level of macrophage activation and the level of viral shedding in influenza virus infection. Our model combines a dynamic model of viral infection, a dynamic model of macrophages and the essential interactions between the virus and macrophages. Our model predicts that the level of macrophage activation can be negatively correlated with the level of viral shedding when viral infectivity is sufficiently high. We further identify that temporary depletion of resting macrophages in response to viral infection is a major driver in our model for the negative relationship between macrophage activation and viral shedding, providing new insight into the mechanisms that regulate macrophage activation. Our model serves as a framework to study the complex dynamics of virus-macrophage interactions and provides a mechanistic explanation for existing experimental observations, contributing to an enhanced understanding of the role of macrophages in influenza viral infection.
A Systematic Review of Intimate Partner Violence Interventions Impacting South Asian Women in the United States

This systematic review is the first published attempt to synthesize literature pertaining to intimate partner violence (IPV) interventions impacting South Asian women in the United States. Applying the conceptual framework of intersectionality, the goals of this review are to (1) understand current trends, intervention modalities, and areas of focus within IPV interventions targeting South Asian communities in the United States and (2) to identify gaps in the address of IPV among these communities. Using the Cochrane Handbook and Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, we searched 35 databases and identified 12 research studies. Our study included a collective sample of 318 South Asian IPV survivors and 25 organizations. Findings underscore that there are minimal IPV interventions available to South Asian women living in the United States. Most interventions have not been systematically evaluated, making their efficacy questionable. Those that reported outcome evaluation, namely recurrence of IPV, demonstrated limited efficacy. IPV research on South Asian women often dismisses financial concerns in light of cultural dimensions impacting IPV. Given that financial dependence is a major driver of violence against South Asian women, scholars must question the efficacy of available interventions that cannot foster the social and economic security of IPV survivors. Without sufficient attention to the intersecting social, cultural, and economic challenges that South Asian women face in abusive relationships, the efficacy of IPV interventions will remain limited.
Evaluation of biomechanically corrected intraocular pressure using Corvis ST and comparison of the Corvis ST, noncontact tonometer, and Goldmann applanation tonometer in patients with glaucoma

Purpose The aim of the study was to investigate the effects of various anatomical structures on intraocular pressure (IOP) measurements obtained by the Corneal Visualization Scheimpflug Technology (Corvis ST), Goldmann applanation tonometer (GAT), and noncontact tonometer (NCT), as well as to assess the interchangeability among the four types of IOP measurement: IOP-GAT, IOP-NCT, IOP-Corvis, and biomechanically corrected IOP (bIOP-Corvis), with a particular focus on bIOP-Corvis. Materials and methods We included 71 patients with primary open-angle glaucoma and assessed their IOP measurements obtained with the GAT, NCT, and Corvis ST using a repeated measures ANOVA, a paired t-test with Bonferroni correction, stepwise multiple regression analyses and Bland–Altman plots. Results IOP-GAT showed the highest values (13.5 ± 2.1 mmHg [mean ± standard deviation]), followed by IOP-NCT (13.2 ± 2.7 mmHg), IOP-Corvis (10.6 ± 2.8 mmHg), and bIOP-Corvis (10.0 ± 2.3 mmHg). With exceptions of bIOP-Corvis and IOP-GAT, all IOP variations were explained by regression coefficients involving the central corneal thickness. Bland–Altman plots showed a mean difference between IOP-GAT and the other IOP measurements (IOP-Corvis, bIOP-Corvis, and IOP-NCT), which were -2.90, -3.48, and -0.29 mmHg, respectively. The widths of the 95% limits of agreement between all pairs of IOP measurements were greater than 3 mmHg. Conclusion IOP values obtained with the Corvis ST, NCT, and GAT were not interchangeable. The bIOP-Corvis measurement corrected for the ocular structure.
A Bayesian Hierarchical Framework for Pathway Analysis in Genome-Wide Association Studies

Background: Pathway analysis allows joint consideration of multiple SNPs belonging to multiple genes, which in turn belong to a biologically defined pathway. This type of analysis is usually more powerful than single-SNP analyses for detecting joint effects of variants in a pathway. Methods: We develop a Bayesian hierarchical model by fully modeling the 3-level hierarchy, namely, SNP-gene-pathway that is naturally inherent in the structure of the pathways, unlike the currently used ad hoc ways of combining such information. We model the effects at each level conditional on the effects of the levels preceding them within the generalized linear model framework. To deal with the high dimensionality, we regularize the regression coefficients through an appropriate choice of priors. The model is fit using a combination of iteratively weighted least squares and expectation-maximization algorithms to estimate the posterior modes and their standard errors. A normal approximation is used for inference. Results: We conduct simulations to study the proposed method and find that our method has higher power than some standard approaches in several settings for identifying pathways with multiple modest-sized variants. We illustrate the method by analyzing data from two genome-wide association studies on breast and renal cancers. Conclusion: Our method can be helpful in detecting pathway association.
Comparison of Spinal Cord Stimulation Waveforms for Treating Chronic Low Back Pain: Systematic Review and Meta-Analysis.

BACKGROUND The treatment of chronic refractory low back pain (LBP) is challenging. Conservative and pharmacologic options have demonstrated limited efficacy. Spinal cord stimulation (SCS) has been shown to be effective in reducing chronic LBP in various contexts. With emerging SCS technologies, the collective evidence of novel waveforms relative to traditional tonic stimulation for treating chronic LBP has yet to be clearly characterized. OBJECTIVES To provide evidence for various SCS waveforms-tonic, burst, and high frequency (HF)-relative to each other for treating chronic LBP. STUDY DESIGN Systematic review and meta-analysis. METHODS PubMed, Medline, Cochrane Library, prior systematic reviews, and reference lists were screened by 2 separate authors for all randomized trials and prospective cohort studies comparing different SCS waveforms for treatment of chronic LBP. RESULTS We identified 11 studies that included waveform comparisons for treating chronic LBP. Of these, 6 studies compared burst versus tonic, 2 studies compared burst versus HF, and 3 studies compared tonic versus HF. A meta-analysis of 5 studies comparing burst versus tonic was conducted and revealed pooled superiority of burst over tonic in pain reduction. One study comparing burst versus tonic was excluded given technical challenges in data extraction. LIMITATIONS Both randomized controlled trials and prospective cohort studies were included for meta-analysis. Several studies included a high risk of bias in at least one domain. CONCLUSIONS Burst stimulation is superior to tonic stimulation for treating chronic LBP. However, superiority among other waveforms has yet to be clearly established given some heterogeneity and limitations in evidence. Given the relative novelty of burst and HF SCS waveforms, evidence of longitudinal efficacy is needed.
Clinicopathological and immunohistochemical study of mismatch repair gene (hMLH1 and hMSH2) expression in colorectal carcinoma of young Egyptian patients

Background Mismatch repair gene (MMR) mutations result in microsatellite instability. Microsatellite instability is seen in virtually all cases of hereditary nonpolyposis colorectal cancer (HNPCC), ∼15% of sporadic cases, and in more than 70% of colorectal carcinoma (CRC) cases in young patients. Objective The present study aimed at evaluating the immunohistochemical expression of human mutL homolg 1 (hMLH1) and human mutS homolog 2 (hMSH2) in young Egyptian patients with CRC in an attempt to identify the frequency of MMR gene loss as well as the associated clinicopathological criteria and to try and map out some genetic errors in those patients. Patients and methods The study included 100 Egyptian patients younger than 50 years with CRC, recruited from Ain Shams University Hospitals in the period between March 2006 and June 2010. All patients were scheduled for surgical resections of their tumors. All colectomy specimens were subjected to routine pathological examination as well as immunohistochemical staining for the protein products of hMLH1 and hMSH2. Results Among the 100 patients, 7% had a positive family history of CRC, 34% had right-sided tumors, 70% had conventional adenocarcinomas, 5% had signet ring cell carcinomas, and 25% had mucinous adenocarcinomas. In total, 47% of tumors belonged to grade III, including 42 cases of adenocarcinoma and five cases of signet ring cell carcinoma. Lymph node metastases were found in 67% of patients. Synchronous polyps were encountered in 10% of patients, and synchronous cancer in the ascending colon was also found in one patient (1%). Loss of expression of hMLH1 and/or hMSH2 was encountered in 31% of patients and they constituted the mutant group. Statistically significant correlations were observed in the mutant group with a positive family history, right-sided tumors, grade III tumors (P<0.05), and mucinous tumors (P<0.01). Moreover, statistically significant correlations were observed in male patients of the hMLH1 mutant group, in whom lymph node metastasis (P<0.01) was absent. Conclusion From this study we can conclude the following:There is a lower prevalence of HNPCC among young Egyptian CRC patients (31%) compared with Western CRC patients (45%) of the same age group.There is a high prevalence of loss of MMR genes in patients with a positive family history of CRC.The main pathological features of HNPCC in Egyptian patients include the increased incidence of mucinous carcinoma, right-sided tumors, synchronous polyps, and a high tumor grade, along with decreased incidence of lymph node metastasis.
Possible Role of Non-Structural Carbohydrates in Alternate Bearing of Pistachio

Summary The alteration of heavy and light yield in pistachio (Pistacia vera L.) has been reported to result from the abscission of flower buds on heavily yielding trees during the summer, but the regulatory mechanisms involved in this bud abscission remain unclear. The present study was conducted to examine the role of nonstructural carbohydrates in flower bud abscission. Carbohydrates (glucose, fructose, sucrose and starch) content was measured in flower buds, leaves, fruits, current shoots, one year old shoots and roots of eight ‘OFF’ and eight ‘ON’ 30 year old pistachio cv. ‘Owhadi’ trees at monthly intervals between flowering and harvest. The flower bud abscission percentage was recorded every 15 day during seed growth. The amounts of soluble sugars and starch were relatively similar in many organs both in ‘OFF’ and ‘ON’ trees until 70 days after bloom. Thereafter, the amount of soluble sugars and starch in 'ON' trees declined in many organs during nut development. During the same period, various organs of ‘OFF’ trees began to accumulate greater concentration of soluble sugars and starch and surpassed the amount measured in those of ‘ON’ trees. There was a high and significant negative correlation between bud, leaf and root sucrose and fruit glucose and flower bud abscission. This indicates that soluble sugars in the many part of tree could be related to the alternate bearing in pistachio.
Exenatide and Renal Outcomes in Patients with Type 2 Diabetes and Diabetic Kidney Disease

Background: Cardiovascular outcomes in clinical trials with type 2 diabetes mellitus (T2DM) patients have shown that glucagon-like peptide-1 receptor agonist can have a beneficial effect on the kidney. This trial aimed to assess the effects of exenatide on renal outcomes in patients with T2DM and diabetic kidney disease (DKD). Methods: We performed a randomized parallel study encompassing 4 general hospitals. T2DM patients with an estimated glomerular filtration rate (eGFR) ≥30 mL/min/1.73 m2 and macroalbuminuria, defined as 24-h urinary albumin excretion rate (UAER) >0.3 g/24 h were randomized 1:1 to receive exenatide twice daily plus insulin glargine (intervention group) or insulin lispro plus glargine (control group) for 24 weeks. The primary outcome was the UAER percentage change from the baseline after 24 weeks of intervention. The rates of hypoglycemia, adverse events (AEs), and change in eGFR during the follow-up were measured as safety outcomes. Results: Between March 2016 and April 2019, 92 patients were randomized and took at least 1 dose of the study drug. The mean age of the participants was 56 years. At baseline, the median UAER was 1,512.0 mg/24 h and mean eGFR was 70.4 mL/min/1.73 m2. After 24 weeks of treatment, the UAER percentage change was significantly lower in the intervention group than in the control group (p = 0.0255). Moreover, the body weight declined by 1.3 kg in the intervention group (the difference between the 2 groups was 2.7 kg, p = 0.0001). Compared to the control group, a lower frequency of hypoglycemia and more gastrointestinal AEs were observed in the intervention group. Conclusion: Exenatide plus insulin glargine treatment for 24 weeks resulted in a reduction of albuminuria in T2DM patients with DKD.
Ovipositional and flight behavior of overwintered Colorado potato beetle (Coleoptera : Chrysomelidae)

Overwintered Colorado potato beetles, Leptinotarsa decemlineata (Say), collected from the soil at South Deerfield, Mass. , in the spring of 1989 were brought to the laboratory and individually fed potato foliage or left unfed. Beetles were tethered to a flight mill for 1h daily to measure the number of flights, their distances, and time per flight when on the mill. Unfed beetles flew more often, for longer periods, and for greater distances (on average, a total of 4,879 m for unfed females compared with 1,346 m for fed females). Many (17 of 27) fed beetles flew for short distances (>5 m) before initiating oviposition; a smaller number (6 of 22) flew >200 m during any flight bout before laying their first eggs. Unfed female beetles laid virtually no eggs, whereas fed females laid an average of 22 eggs/d. Overwintered females that were unmated in the spring did not differ in egg production from spring-mated females, but egg viability was significantly higher. Results show that a single overwintered female constitutes a mobile and fecund founder of populations. The complex life history of the Colorado potato beetle uses migration and diapause to distribute offspring over space and time, thus minimizing reproductive risk.
G-Quadruplexes in the Archaea Domain

The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
Modified Atmosphere and Humidity Film Reduces Browning Susceptibility of Oriental Melon Suture Tissue during Cold Storage

Oriental melons have a relatively short shelf life as they are harvested during the summer season and susceptible to cold-induced injuries. Typical chilling injury when stored at 4 °C is expressed as browning of the fruit suture. To prolong the shelf life and reduce browning of the fruit, the effects of modified atmosphere packaging (MAP), X-tend modified atmosphere (MA)/modified humidity (MH) bulk packaging (XF), and polyethylene (PE) packaging, on oriental melons were investigated during storage at 4 °C and 10 °C for 14 days and under retail display conditions at 20 °C. The O2 concentrations in PE packages stored at 4 °C and 10 °C ranged from 17.4 to 18.5%, whereas those in XF packages were reduced to 16.3–16.6%. The CO2 content of XF package (4.2–4.6%) was higher than that of PE package (1.4–1.9%) stored at 4 °C or 10 °C. Relative humidity (RH) saturated in the PE packages but not in the XF packages after seven days of storage. Furthermore, PE packages performed better at maintaining melon weight and firmness than XF packages during storage at 10 °C for 14 days and under retail display conditions at 20 °C. PE and XF packages effectively reduced the browning index of the peel and white linear sutures of oriental melons compared with the unpackaged control during cold storage at 4 °C, and this observation was maintained at the retail display condition at 20 °C. The enhanced CO2 levels, reduced O2 levels, and optimal RH values that were provided by the MAP, prevented the browning symptoms, and improved the marketability and shelf life of oriental melons.
Sex differences in integrated neuro-cardiovascular control of blood pressure following acute intermittent hypercapnic-hypoxia.

Repetitive hypoxic apneas, similar to that observed in sleep apnea, result in resetting of the sympathetic baroreflex to higher blood pressures (BP). This baroreflex resetting is associated with hypertension in preclinical models of sleep apnea (intermittent hypoxia, IH); however, the majority of understanding comes from males. There are data to suggest female rats exposed to IH do not develop high BP. Clinical data further support sex differences in the development of hypertension in sleep apnea, but mechanistic data are lacking. Herein we examined sex-related differences in the effect of IH on sympathetic control of BP in humans. We hypothesized following acute IH, we would observe a rise in muscle sympathetic nerve activity (MSNA) and arterial BP in young men (n=30) which would be absent in young women (n=19). BP and MSNA were measured during normoxic rest prior to and following 30-minutes of IH. Baroreflex sensitivity (modified Oxford) was evaluated before and after IH. A rise in mean BP following IH was observed in men (+2.0±0.7 mmHg, p=0.03), whereas no change was observed in women (-2.7±1.2 mmHg, p=0.11). The elevation in MSNA following IH was not different between groups (4.7±1.1 vs 3.8±1.2 bursts/min, p=0.65). Sympathetic baroreflex sensitivity did not change following IH in either group (p>0.05). Our results support sex-related differences in the effect of IH on neurovascular control of BP and show any BP-raising effects of IH are absent in young women. These data enhance our understanding of sex-specific mechanisms which may contribute to BP changes in sleep apnea.
Elaeocarpus in Australia and New Zealand

An account of the species of Elaeocarpus from Australia (with Lord Howe Island) and New Zealand is offered, integrated as far as possible with previous findings from Papuasia. Four new species are proposed: E. linsmithii Guymer, and E. carolinae, E. elliffii & E. thelmae Hyland & Coode. One further new species known only in fruit is indicated, and some new informal groups. E. drymophilus Domin & E. grandis F. Muell. are reduced to synonymy under E. angustifolius Bl. ; E. michaelii C. T. White reduced to E. culminicola Warb. Seeds are discussed, as is the occurrence of seed-types not so far noted elsewhere in the genus.
Does microclimate under grey hail protection net affect biological and nutritional properties of ‘Duke’ highbush blueberry (Vaccinium corymbosum L.)?

Introduction. We tested whether the microclimate under grey hail protection nets (HPN) had an influence on the phenology, vegetative and reproductive potential, and fruit quality traits of ’Duke’ highbush blueberry (Vaccinium corymbosum L.) in two consecutive years (2013, 2014). Materials and methods. Light intensity, air temperature and relative humidity were evaluated together with biological properties (flowering and ripening time, bush height and volume, number of flowers and fruits per bush, fruit set percentage, and yield per bush), and fruit quality including biometrical (fruit weight, index of fruit shape and number of seeds per fruit) and nutritional (soluble solid content – SSC, titratable acidity – TA, total anthocyanins content – TACY, total phenolic content – TPC and total antioxidant capacity – TAC) parameters. Results and discussion. In both seasons, light was reduced by 5–20% under HPN, whereas daily maximum temperature was 2.4 °C higher in the open field (OF). This caused two days earlier ripening time in OF compared to the HPN. The increased yield per bush under HPN was the result of larger fruit weight. SSC were unaffected by the net in 2013 while in 2014 significantly higher value of SSC was registered under HPN compared to OF. Although apparent differences in TACY and TPC were not observed between the treatments, TAC significantly increased under HPN in 2014. Conclusion. The use of grey HPN could be considered as a suitable alternative for the hail protection of highbush blueberry ensuring an increased fruit production without negative effects on their quality.