Miracle-dz/UniFAR-FTUs huggingface dataset:
Penicillin Induced Persistence in Chlamydia trachomatis: High Quality Time Lapse Video Analysis of the Developmental Cycle

Background Chlamydia trachomatis is a major human pathogen with a unique obligate intracellular developmental cycle that takes place inside a modified cytoplasmic structure known as an inclusion. Following entry into a cell, the infectious elementary body (EB) differentiates into a non - infectious replicative form known as a reticulate body (RB). RBs divide by binary fission and at the end of the cycle they redifferentiate into EBs. Treatment of C.trachomatis with penicillin prevents maturation of RBs which survive and enlarge to become aberrant RBs within the inclusion in a non - infective persistent state. Persistently infected individuals may be a reservoir for chlamydial infection. The C.trachomatis genome encodes the enzymes for peptidoglycan (PG) biosynthesis but a PG sacculus has never been detected. This coupled to the action of penicillin is known as the chlamydial anomaly. We have applied video microscopy and quantitative DNA assays to the chlamydial developmental cycle to assess the effects of penicillin treatment and establish a framework for investigating penicillin induced chlamydial persistence. Principal Findings Addition of penicillin at the time of cell infection does not prevent uptake and the establishment of an inclusion. EB to RB transition occurs but bacterial cytokinesis is arrested by the second binary fission. RBs continue to enlarge but not divide in the presence of penicillin. The normal developmental cycle can be recovered by the removal of penicillin although the large, aberrant RBs do not revert to the normal smaller size but remain present to the completion of the developmental cycle. Chromosomal and plasmid DNA replication is unaffected by the addition of penicillin but the arrest of bacterial cytokinesis under these conditions results in RBs accumulating multiple copies of the genome. Conclusions We have applied video time lapse microscopy to the study of the chlamydial developmental cycle. Linked with accurate measures of genome replication this provides a defined framework to analyse the developmental cycle and to investigate and provide new insights into the effects of antibiotic treatments. Removal of penicillin allows recovery of the normal developmental cycle by 10–20 hrs and the process occurs by budding from aberrant RBs.
Designing and evaluating an automated system for real-time medication administration error detection in a neonatal intensive care unit

Abstract Background Timely identification of medication administration errors (MAEs) promises great benefits for mitigating medication errors and associated harm. Despite previous efforts utilizing computerized methods to monitor medication errors, sustaining effective and accurate detection of MAEs remains challenging. In this study, we developed a real-time MAE detection system and evaluated its performance prior to system integration into institutional workflows. Methods Our prospective observational study included automated MAE detection of 10 high-risk medications and fluids for patients admitted to the neonatal intensive care unit at Cincinnati Children’s Hospital Medical Center during a 4-month period. The automated system extracted real-time medication use information from the institutional electronic health records and identified MAEs using logic-based rules and natural language processing techniques. The MAE summary was delivered via a real-time messaging platform to promote reduction of patient exposure to potential harm. System performance was validated using a physician-generated gold standard of MAE events, and results were compared with those of current practice (incident reporting and trigger tools). Results Physicians identified 116 MAEs from 10 104 medication administrations during the study period. Compared to current practice, the sensitivity with automated MAE detection was improved significantly from 4.3% to 85.3% (P = .009), with a positive predictive value of 78.0%. Furthermore, the system showed potential to reduce patient exposure to harm, from 256 min to 35 min (P < .001). Conclusions The automated system demonstrated improved capacity for identifying MAEs while guarding against alert fatigue. It also showed promise for reducing patient exposure to potential harm following MAE events.
Temporal Stability of the Ford Insomnia Response to Stress Test (FIRST).

STUDY OBJECTIVES The Ford Insomnia Response to Stress Test (FIRST) is a self-report tool that measures sleep reactivity (i.e., vulnerability to experience situational insomnia under stressful conditions). Sleep reactivity has been termed a "trait-like" vulnerability; however, evidence of its long-term stability is lacking. The main objective of the current psychometric study was to investigate the temporal stability of the FIRST over two 6-mo intervals in a population-based sample of adults with and without insomnia. The temporal stability of the FIRST was also compared with the temporal stability of other scales associated with insomnia (trait-anxiety, arousability). METHODS Participants included 1,122 adults (mean age = 49.9 y, standard deviation = 14.8; 38.8% male) presenting with an insomnia syndrome (n = 159), insomnia symptoms (n = 152), or good sleep (n = 811). Participants completed the FIRST, the State-Trait Anxiety Inventory (trait-anxiety), and the Arousal Predisposition Scale (arousability) on three different occasions: baseline and at 6- and 12-mo follow-up. Intraclass correlation coefficients (ICCs) were computed for all scales (baseline to 6 mo and 6 to 12 mo). RESULTS The FIRST yielded strong temporal stability from baseline to 6 mo among those with insomnia syndrome (ICC = 0.81), symptoms (ICC = 0.78), and good sleep (ICC = 0.81). Similar results were observed for 6 to 12 mo among those with insomnia syndrome (ICC = 0.74), insomnia symptoms (ICC = 0.82), and good sleep (ICC = 0.84). The stability of the FIRST was not comparable with the stability of trait-anxiety, but was somewhat comparable with the stability of arousability. CONCLUSIONS Overall, the FIRST is a temporally reliable stable scale over 6-mo intervals. Future research is needed to corroborate the stability and trait-like measures of sleep reactivity with physiological, behavioural and personality measures.
Natural Selection of Human Embryos: Decidualizing Endometrial Stromal Cells Serve as Sensors of Embryo Quality upon Implantation

Background Pregnancy is widely viewed as dependent upon an intimate dialogue, mediated by locally secreted factors between a developmentally competent embryo and a receptive endometrium. Reproductive success in humans is however limited, largely because of the high prevalence of chromosomally abnormal preimplantation embryos. Moreover, the transient period of endometrial receptivity in humans uniquely coincides with differentiation of endometrial stromal cells (ESCs) into highly specialized decidual cells, which in the absence of pregnancy invariably triggers menstruation. The role of cyclic decidualization of the endometrium in the implantation process and the nature of the decidual cytokines and growth factors that mediate the crosstalk with the embryo are unknown. Methodology/Principal Findings We employed a human co-culture model, consisting of decidualizing ESCs and single hatched blastocysts, to identify the soluble factors involved in implantation. Over the 3-day co-culture period, approximately 75% of embryos arrested whereas the remainder showed normal development. The levels of 14 implantation factors secreted by the stromal cells were determined by multiplex immunoassay. Surprisingly, the presence of a developing embryo had no significant effect on decidual secretions, apart from a modest reduction in IL-5 levels. In contrast, arresting embryos triggered a strong response, characterized by selective inhibition of IL-1β, -6, -10, -17, -18, eotaxin, and HB-EGF secretion. Co-cultures were repeated with undifferentiated ESCs but none of the secreted cytokines were affected by the presence of a developing or arresting embryo. Conclusions Human ESCs become biosensors of embryo quality upon differentiation into decidual cells. In view of the high incidence of gross chromosomal errors in human preimplantation embryos, cyclic decidualization followed by menstrual shedding may represent a mechanism of natural embryo selection that limits maternal investment in developmentally impaired pregnancies.
Primary Sjögren's syndrome with diffuse cystic lung changes developed systemic lupus erythematosus: a case report and literature review

Sjögren's syndrome (SS) is a chronic inflammatory autoimmune disease that can occur as a unique existence (primary Sjögren's syndrome) or merge with other systemic diseases like systemic lupus erythematosus (SLE), rheumatoid arthritis or systemic sclerosis (secondary Sjögren's syndrome). Data on the two diseases occurrence order are inadequate. Primary Sjögren's syndrome (pSS) may relatively uncommonly lead to diffuse cystic lung changes. We represent a female who was diagnosed pSS with diffuse cystic lung alterations developed SLE two years later. SS was diagnosed on account of the existence of dryness of eye and mouth, Schirmer's test, biopsy of the minor salivary glands of her lip, positive anti-SSA and anti-SSB antibody in the serum. Chest computed tomography image showed bilateral diffuse cystic changes with a wide variation in cyst size and distribution. SLE was finally diagnosed based on bilateral lower limb skin rash, gonarthritis and omarthritis, low level of complement, antinuclear antibody 1:640 and positive antibodies to double-stranded DNA. Improvement was achieved with therapy of corticosteroids, hydroxychloroquine and antibiotics. This report provides us clinical, diagnosis and treatment perception of SS-onset SLE as patient presenting diffuse cystic lung changes.
Functional capacity and health-related quality of life outcomes post transcatheter aortic valve replacement: a systematic review and meta-analysis

Background transcatheter aortic valve replacement (TAVR) provides prognostic benefit for high surgical-risk patients with severe aortic stenosis (AS), yet the impact to patient outcomes is far less understood. Method we performed a systematic review and meta-analysis to evaluate functional capacity and health-related quality of life (HRQoL) outcomes for patients up to 12 months post TAVR. A total of 20 eligible publications, comprising randomised-controlled trials, observational studies and a registry study were identified from electronic databases, including MEDLINE, EMBASE, Cochrane Library and others (inception to February 2017). Results the total sample was 2,775 with a mean age of 81.8 ± 2.1 years, more than half (52%) were female and high surgical risk 9.6 ± 4.3% mean STS (Society of Thoracic Surgeons risk model). Post TAVR, patients had significant improvement in functional capacity of >40 m in the 6-minute walk test (6MWT) (95% confidence interval (CI) 9.69-73.28) and a clinically meaningful increase in ability to perform daily physical-based tasks (Duke Activity Status Index (DASI), mean difference (MD) increase 5.42 points, 95% CI 3.16-7.68). HRQoL improved consistently following TAVR regardless of measure used. Significant increases occurred in the physical component summary scores (PCS) of the short form (SF) health surveys (MD increase 10.45 (SF36) and 10.14 (SF12) points). Conclusion functional capacity and HRQoL improved substantially following TAVR, despite evolving patient selection criteria, thus TAVR continues to provide a directly beneficial option for severe AS patients.
Codebook driven short-term predictor parameter estimation for speech enhancement

In this paper, we present a new technique for the estimation of short-term linear predictive parameters of speech and noise from noisy data and their subsequent use in waveform enhancement schemes. The method exploits a priori information about speech and noise spectral shapes stored in trained codebooks, parameterized as linear predictive coefficients. The method also uses information about noise statistics estimated from the noisy observation. Maximum-likelihood estimates of the speech and noise short-term predictor parameters are obtained by searching for the combination of codebook entries that optimizes the likelihood. The estimation involves the computation of the excitation variances of the speech and noise auto-regressive models on a frame-by-frame basis, using the a priori information and the noisy observation. The high computational complexity resulting from a full search of the joint speech and noise codebooks is avoided through an iterative optimization procedure. We introduce a classified noise codebook scheme that uses different noise codebooks for different noise types. Experimental results show that the use of a priori information and the calculation of the instantaneous speech and noise excitation variances on a frame-by-frame basis result in good performance in both stationary and nonstationary noise conditions.
The Role of Rituximab in Chronic Lymphocytic Leukemia Treatment and the Potential Utility of Biosimilars.

Chronic lymphocytic leukemia (CLL) is managed with observation for asymptomatic or clinically silent disease; pharmacologic intervention is generally required for symptomatic patients with clinically significant adenopathy or cytopenia. In the front-line treatment of CLL, the current standard-of-care includes chemotherapy in combination with an anti-CD20 monoclonal antibody (e.g., rituximab, ofatumumab, or obinutuzumab) or ibrutinib as single agent. Despite the evolving treatment paradigm toward targeted therapy, it is likely that rituximab (plus chemotherapy), with or without targeted agents, will retain a significant role in CLL treatment. However, patents for many biologics, including rituximab, have expired or will expire in the near future. Furthermore, access to rituximab has remained challenging, particularly in countries with restricted resources. Together, these concerns have prompted the development of safe and effective rituximab biosimilars. The term "biosimilar" refers to a biologic that is highly similar to an approved reference (originator) product, notwithstanding minor differences in clinically inactive components, and for which there are no clinically meaningful differences in purity, potency, or safety. Biosimilars are developed to treat the same condition(s) using the same treatment regimens as an approved reference biologic and have the potential to increase access to more affordable treatments. We review the importance of rituximab in the current treatment of CLL, the scientific basis of its future role in combination with chemotherapy, and the role of new and emerging agents in the treatment of CLL, which could potentially be used in combination with rituximab biosimilars. We also discuss rituximab biosimilars currently in development. IMPLICATIONS FOR PRACTICE Front-line treatments for chronic lymphocytic leukemia (CLL) include chemotherapy in combination with an anti-CD20 monoclonal antibody (e.g., rituximab, ofatumumab, or obinutuzumab) or ibrutinib as single agent. Despite the evolving treatment paradigm, it is likely rituximab (plus chemotherapy) and targeted agents undergoing clinical evaluation will retain a significant role in CLL treatment. However, patents for many biologics, including rituximab, have expired or will expire in the near future and, in many regions, access to rituximab remains challenging. Together, these concerns have prompted the development of safe and effective rituximab biosimilars, with the potential to increase access to more affordable treatments.
The Prevalence and Risk Factors of Renal Insufficiency among Korean HIV-Infected Patients: The Korea HIV/AIDS Cohort Study

Background Renal disease is one of the leading causes of morbidity and mortality among people infected with human immunodeficiency virus (HIV). However, there are very few published studies about renal insufficiency in HIV-infected persons in Asia, especially in South Korea. Materials and Methods A cross-sectional study was performed to investigate the prevalence and risk factors of renal insufficiency, defined as <60 mL/min/1.73 m2, in subjects in the Korea HIV/AIDS Cohort Study enrolled from 19 institutions between December 2006 and July 2013. Data at entry into the cohort were analyzed. Results Of 454 enrolled subjects, 24 (5.3%) showed renal insufficiency at entry into the cohort. The mean age of patients in the renal insufficiency group was 5.28 years and the majority were male subjects (91.7%). All the patients were receiving antiretroviral agents, mostly protease inhibitor-based regimens (76.4%), for an average of 19 months. In univariate analysis, older age (P = 0.002), diabetes mellitus (DM) (P = 0.0002), unknown route of transmission (P = 0.007), and taking indinavir (P = 0.0022) were associated with renal insufficiency. In multivariable analysis, older age [odds ratio (OR) 1.07, 95% confidence interval (CI) 1.03–1.12, P = 0.002], DM [OR 3.03, 95% CI 1.17–7.82, P = 0.022], unknown route of transmission [OR 6.15, 95% CI 1.77–21.33, P = 0.004], and taking indinavir [OR 3.07, 95% CI 1.17–8.05, P = 0.023] were independent risk factors of renal insufficiency. Conclusion The prevalence of renal insufficiency in HIV-infected subjects in this study was relatively low, similar to that in other countries. Aging, DM, and taking indinavir were significantly associated with decreased glomerular filtration rate. Furthermore, unknown route of transmission was an independent risk factor, which was interpreted as a reflection of patient compliance. Further studies on the incidence and risk factors of renal insufficiency during HIV infection using follow-up cohort data are necessary.
Morphological Diversity and the Roles of Contingency, Chance and Determinism in African Cichlid Radiations

Background Deterministic evolution, phylogenetic contingency and evolutionary chance each can influence patterns of morphological diversification during adaptive radiation. In comparative studies of replicate radiations, convergence in a common morphospace implicates determinism, whereas non-convergence suggests the importance of contingency or chance. Methodology/Principal Findings The endemic cichlid fish assemblages of the three African great lakes have evolved similar sets of ecomorphs but show evidence of non-convergence when compared in a common morphospace, suggesting the importance of contingency and/or chance. We then analyzed the morphological diversity of each assemblage independently and compared their axes of diversification in the unconstrained global morphospace. We find that despite differences in phylogenetic composition, invasion history, and ecological setting, the three assemblages are diversifying along parallel axes through morphospace and have nearly identical variance-covariance structures among morphological elements. Conclusions/Significance By demonstrating that replicate adaptive radiations are diverging along parallel axes, we have shown that non-convergence in the common morphospace is associated with convergence in the global morphospace. Applying these complimentary analyses to future comparative studies will improve our understanding of the relationship between morphological convergence and non-convergence, and the roles of contingency, chance and determinism in driving morphological diversification.
Relationship Between Anti-Felting Properties and Physicochemical Properties of Wool Treated with Low-Temperature Plasma

Low-temperature plasma treatment, which offers an alternative to the existing treatment using chlorine, has been drawing worldwide attention as an eco-friendly technology for the anti-felting of wool. However, the reason why that plasma-treated wool does not shrink even after repeated aqueous laundry has still not been elucidated, though a number of related papers have been published. The aim of this study is to explore the reason by analyzing the surface of Ar-plasma treat wool using FT-IR and also XPS and by examining the changes of physicochemical properties of plasma-treated wool. It is suggested that intermediate cystine oxides(i.e., -S(O)-S- and -S(O)2-S- groups generated on the wool fiber surface) have a strong affinity with water. Subsequently, cohesive force is exerted between fiber surfaces and this results in a decrease of the flexibility of the individual fiber in assembly. Therefore, any entanglements between fibers are suppressed, and the felting is controlled. This is an important anti-felting property plasma treatment provided. In addition, carboxyl and sulphonic acid groups produced on the fiber surface play some part in the felting behavior of wool probably due to an increase in the hydration of the fiber surface.
Human RTEL1 stabilizes long G-overhangs allowing telomerase-dependent over-extension

Abstract Telomere maintenance protects the cell against genome instability and senescence. Accelerated telomere attrition is a characteristic of premature aging syndromes including Dyskeratosis congenita (DC). Mutations in hRTEL1 are associated with a severe form of DC called Hoyeraal-Hreidarsson syndrome (HHS). HHS patients carry short telomeres and HHS cells display telomere damage. Here we investigated how hRTEL1 contributes to telomere maintenance in human primary as well as tumor cells. Transient depletion of hRTEL1 resulted in rapid telomere shortening only in the context of telomerase-positive cells with very long telomeres and high levels of telomerase. The effect of hRTEL1 on telomere length is telomerase dependent without impacting telomerase biogenesis or targeting of the enzyme to telomeres. Instead, RTEL1 depletion led to a decrease in both G-overhang content and POT1 association with telomeres with limited telomere uncapping. Strikingly, overexpression of POT1 restored telomere length but not the overhang, demonstrating that G-overhang loss is the primary defect caused by RTEL1 depletion. We propose that hRTEL1 contributes to the maintenance of long telomeres by preserving long G-overhangs, thereby facilitating POT1 binding and elongation by telomerase.
Patterns on serpentine shapes elicit visual attention in marmosets (Callithrix jacchus)

Given the prevalence of threatening snakes in the evolutionary history, and modern‐day environments of human and nonhuman primates, sensory, and perceptual abilities that allow for quick detection of, and appropriate response to snakes are likely to have evolved. Many studies have demonstrated that primates recognize snakes faster than other stimuli, and it is suggested that the unique serpentine shape is responsible for its quick detection. However, there are many nonthreatening serpentine shapes in the environment (e.g., vines) that are not threatening; therefore, other cues must be used to distinguish threatening from benign serpentine objects. In two experiments, we systematically evaluated how common marmosets (Callithrix jacchus) visually attend to specific snake‐like features. In the first experiment, we examined if skin pattern is a cue that elicits increased visual inspection of serpentine shapes by measuring the amount of time the marmosets looked into a blind before, during, and after presentation of clay models with and without patterns. The marmosets spent the most time looking at the objects, both serpentine and triangle, that were etched with scales, suggesting that something may be uniquely salient about scales in evoking attention. In contrast, they showed relatively little interest in the unpatterned serpentine and control (a triangle) stimuli. In experiment 2, we replicated and extended the results of experiment 1 by adding additional stimulus conditions. We found that patterns on a serpentine shape generated more inspection than those same patterns on a triangle shape. We were unable to confirm that a scaled pattern is unique in its ability to elicit visual interest; the scaled models elicited similar looking times as line and star patterns. Our data provide a foundation for future research to examine how snakes are detected and identified by primates. Am. J. Primatol. 78:928–936, 2016. © 2016 Wiley Periodicals, Inc.