Miracle-dz/UniFAR-FTUs huggingface dataset:
A High-Resolution Map of Meiotic Recombination in Cryptococcus deneoformans Demonstrates Decreased Recombination in Unisexual Reproduction

Multiple species within the basidiomycete genus Cryptococcus cause cryptococcal disease. These species are estimated to affect nearly a quarter of a million people leading to ∼180,000 mortalities, annually. Sexual reproduction, which can occur between haploid yeasts of the same or opposite mating type, is a potentially important contributor to pathogenesis as recombination can generate novel genotypes and transgressive phenotypes. However, our quantitative understanding of recombination in this clinically important yeast is limited. Here, we describe genome-wide estimates of recombination rates in Cryptococcus deneoformans and compare recombination between progeny from α–α unisexual and a–α bisexual crosses. We find that offspring from bisexual crosses have modestly higher average rates of recombination than those derived from unisexual crosses. Recombination hot and cold spots across the C. deneoformans genome are also identified and are associated with increased GC content. Finally, we observed regions genome-wide with allele frequencies deviating from the expected parental ratio. These findings and observations advance our quantitative understanding of the genetic events that occur during sexual reproduction in C. deneoformans, and the impact that different forms of sexual reproduction are likely to have on genetic diversity in this important fungal pathogen.
Evaluating the core microbiota in complex communities: A systematic investigation

The study of complex microbial communities poses unique conceptual and analytical challenges, with microbial species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a 'core' microbiota approach, focusing only on the stable and permanent members of the community, is becoming increasingly popular. Given the various ways of defining a core microbiota, it is prudent to examine whether the definition of the core impacts upon the results obtained. Here we used complex marine sponge microbiotas and undertook a systematic evaluation of the degree to which different factors used to define the core influenced the conclusions. Significant differences in alpha- and beta-diversity were detected using some but not all core definitions. However, findings related to host specificity and environmental quality were largely insensitive to major changes in the core microbiota definition. Furthermore, none of the applied definitions altered our perception of the ecological networks summarising interactions among bacteria within the sponges. These results suggest that, while care should still be taken in interpretation, the core microbiota approach is surprisingly robust, at least for comparing microbiotas of closely related samples.
HPV16 L1 and L2 DNA methylation predicts high-grade cervical intraepithelial neoplasia in women with mildly abnormal cervical cytology

DNA methylation changes in human papillomavirus type 16 (HPV16) DNA are common and might be important for identifying women at increased risk of cervical cancer. Using recently published data from Costa Rica we developed a classification score to differentiate women with cervical intraepithelial neoplasia grade 2 or 3 (CIN2/3) from those with no evident high‐grade lesions. Here, we aim to investigate the performance of the score using data from the UK. Exfoliated cervical cells at baseline and 6‐months follow‐up were analyzed in 84 women selected from a randomized clinical trial of women undergoing surveillance for low‐grade cytology. Selection of women for the methylation study was based on detectable HPV16 in the baseline sample. Purified DNA was bisulfite converted, amplified and pyrosequenced at selected CpG sites in the viral genome (URR, E6, L1 and L2), with blinding of laboratory personnel to the clinical data. The primary measure was a predefined score combining the mean methylation in L1 and any methylation in L2. At the second follow‐up visit, 73/84 (87%) women were HPV16 positive and of these 25 had a histopathological diagnosis of CIN2/3. The score was significantly associated with CIN2/3 (area under curve = 0.74, p = 0.002). For a cutoff with 92% sensitivity, colposcopy could have been avoided in 40% (95% CI 27–54%) of HPV16 positive women without CIN2/3; positive predictive value was 44% (32–58%) and negative predictive value was 90% (71–97%). We conclude that quantitative DNA methylation assays could help to improve triage among HPV16 positive women.
The transcriptome-wide effects of exposure to a pyrethroid pesticide on the Critically Endangered delta smelt Hypomesus transpacificus

Research into the effects of contaminants on fishes is often conducted on well- studied model test species, whose responses may be different than those of endangered species. We developed an oligonucleotide microarray consisting of 12 595 genes to examine the effects of the pesticide permethrin on an endangered fish in California, USA, the delta smelt Hypomesus transpacificus. The microarray was used in combination with quantitative PCR (qPCR) assess- ments. We exposed larval delta smelt to permethrin for 96 h at concentrations of 0.69, 1.37, 2.56, 4.84, 12.88 and 24.94 µg l �1 , and compared the responses to a control group. The 96 h 50% lethal concentration (LC50) was 4.07 µg l �1 , which is lower than those reported for model test species and similar to other endangered species. With increasing exposure concentration, we detected the dif- ferential expression of 3342 microarray features with elevated expression of genes involved in protein degradation and apoptosis, and decreased expression of immune function genes. Func- tional analysis indicated that genes involved in protein degradation, immune function, an unfolded protein response, meta bolism and cell signaling cascades were affected by exposure to permethrin. Many of the gene responses in the 0.69 µg l �1 treatment group differed in their direc- tional change in expression from those at higher exposure concentrations, suggesting a potential mechanistic threshold of sub-lethal toxicity at concentrations below the lowest observed effect concentration (LOEC) of 2.56 µg l �1 . These results are consistent with non-monotonic response patterns to contaminants, and demonstrate the effects on a sensitive fish species of a widely used pyrethroid pesticide at concentrations below those that affect model test species.
Challenges of Nurses’ Empowerment in the Management of Patient Aggression: A Qualitative Study

Background: Patients' aggression in the mental care setting is a global health problem with major psychological, physical, and economic consequences; nurse empowerment to manage this aggressive behavior is an important step in psychiatric nursing. The aim of this study was to explore psychiatric nurses' experiences of the challenges of empowerment in the management of patients' aggression. Materials and Methods: This qualitative study was performed among 20 nurses working in a major referral psychiatric center in Iran during 2014–2016. The purposive sampling method was used for selecting the participants. Data were collected through semi-structured interviews, observations, and filed notes. Inductive content analysis was used for data analysis. Results: Three categories and ten subcategories were identified: inefficient organizational policy (limited human resources, mandatory shifts, shortage of protective equipment, lack of motivational sparks); insufficient job growth (failure to implement training programs, insufficient effort for job competence, lack of clinical guidelines); and deficiencies in the organizational culture (inadequate autonomy and authority, lack of the culture of prevention, culture of fault and blame after an incident). Conclusions: Psychiatric nurses were not satisfied with organizational empowering conditions for the management of patients' aggression and reported low levels of access to learning opportunity, receiving support and essential resources that led to unnecessary use of containment measures. Managers must make every effort to create organizational context that make it possible to empower nurses for optimal practice.
Milnacipran for the management of fibromyalgia syndrome

Fibromyalgia syndrome (FMS) is a widespread pain condition associated with fatigue, cognitive dysfunction, sleep disturbance, depression, anxiety, and stiffness. Milnacipran is one of three medications currently approved by the Food and Drug Administration in the United States for the management of adult FMS patients. This review is the second in a three-part series reviewing each of the approved FMS drugs and serves as a primer on the use of milnacipran in FMS treatment including information on pharmacology, pharmacokinetics, safety and tolerability. Milnacipran is a mixed serotonin and norepinephrine reuptake inhibitor thought to improve FMS symptoms by increasing neurotransmitter levels in descending central nervous system inhibitory pathways. Milnacipran has proven efficacy in managing global FMS symptoms and pain as well as improving symptoms of fatigue and cognitive dysfunction without affecting sleep. Due to its antidepressant activity, milnacipran can also be beneficial to FMS patients with coexisting depression. However, side effects can limit milnacipran tolerability in FMS patients due to its association with headache, nausea, tachycardia, hyper- and hypotension, and increased risk for bleeding and suicidality in at-risk patients. Tolerability can be maximized by starting at low dose and slowly up-titrating if needed. As with all medications used in FMS management, milnacipran works best when used as part of an individualized treatment regimen that includes resistance and aerobic exercise, patient education and behavioral therapies.
Visual Search With Varying Versus Consistent Attentional Templates: Effects on Target Template Establishment, Comparison, and Guidance

Attentional templates can be represented in visual working memory (VWM) when the target varies from trial-to-trial and can be represented in long-term memory (LTM) when the target is consistent during trial runs. Given that attentional templates can be represented in either VWM or LTM, are there any differences in how these representations impact visual search when targets are consistent compared with varying? The current study tested the consistent template hypothesis, which predicts faster performance with a consistent target compared with a varying target. Experiment 1 examined whether consistent targets could lead to consistent templates that would improve template establishment, guidance, and/or comparison of the template to search items. Search response time was faster for consistent targets, and consistent targets produced faster comparison processes, but not more efficient guidance. Experiment 2 examined the consistent template restoration hypothesis, which predicts faster template establishment and comparison processes for a previously encountered consistent target. Experiment 2 replicated the consistent template hypothesis and supported the consistent template restoration hypothesis. These studies demonstrate that although attentional guidance is similar with varying and consistent attentional templates, consistent templates improve search performance by speeding template establishment and comparison processes.
Association between the functional movement screen and injury development in college athletes.

BACKGROUND As the number of sports participants continues to rise, so does the number of sports injuries. Establishing a valid method of identifying athletes at elevated risk for injury could lead to intervention programs that lower injury rates and improve overall athlete performance. The Functional Movement Screen (FMS)™ is an efficient and reliable method to screen movement patterns during the performance of specific tasks. The purpose of this study is to explore the association between pre-season FMS TM scores and the development of injury in a population of collegiate athletes. STUDY DESIGN Descriptive epidemiology study. METHODS FMS™ scores were obtained for 160 collegiate athletes and injury development was tracked throughout the season. These athletes were both male and female and participated in contact and non-contact sports. Redundancies were utilized with injury data collection, including medical record reviews and interviews with team athletic trainers, to ensure that all injuries requiring medical attention were captured. At the conclusion of the season, a logistic regression analysis was performed to determine which combination of factors best predicted injury. RESULTS Athletes with an FMS™ composite score at 14 or below combined with a self-reported past history of injury were at 15 times increased risk of injury. A positive likelihood ratio of 5.8 was calculated which improved the probability of predicting injury from 33% pretest to 74% posttest. CONCLUSIONS This study adds to the growing body of evidence demonstrating a predictive relationship between FMS™ composite scores and past history of injury with the development of future injury. LEVEL OF EVIDENCE 3, Non-random prospective cohort design.
Does a lack of observed beaked whale strandings in military exercise areas mean no impacts have occurred? A comparison of stranding and detection probabilities in the Canary and main Hawaiian Islands

Anthropogenic activities must be monitored to determine effects on marine mammal species, but the difficulty lies in how to measure impact. Mass strandings of beaked whales have occurred in association with naval exercises, with two species most affected, Cuvier’s (Ziphius cavirostris) and Blainville’s (Mesoplodon densirostris) beaked whales. Six such events have occurred in the Canary Islands but there have been no reported mass strandings in Hawai‘i. We assess the hypothesis that factors that influence the likelihood of strandings occurring and/or being detected differ between the Canary and main Hawaiian Islands, such that beaked whale stranding/detection probabilities will be lower in Hawai‘i. On an archipelago-wide basis, nearshore bathymetric comparisons indicate that the Canaries have a greater proportion and a total greater amount of appropriate beaked whale habitat closer to shore, with a steeper slope. Hawaiian shorelines are more dominated by steep cliffs, human population density is much lower, and human population per kilometer of shoreline is 53% lower than in the Canaries. All of these factors suggest that there is a higher probability of a carcass washing onshore and being detected in the Canary Islands. It cannot be concluded that the lack of mass strandings in Hawai‘i is evidence of no impact.
Transferable Plasmid-Borne mcr-1 in a Colistin-Resistant Shigella flexneri Isolate

ABSTRACT Since the initial discovery of mcr-1 in an Escherichia coli isolate from China, the gene has also been detected in Klebsiella pneumoniae and Salmonella enterica but is rarely reported in other Enterobacteriaceae. Here, we report the isolation and identification of a Shigella flexneri strain harboring mcr-1 from stool samples in a pig farm in China from 2009. The MIC of colistin for the isolate is 4 μg/ml. Conjugation assays showed that the donor S. flexneri strain has functional and transferable colistin resistance. Sequencing revealed that mcr-1 was present on a putative composite transposon flanked by inverted repeats of ISApl1. IMPORTANCE There are four species of Shigella, and Shigella flexneri is the most frequently isolated species in low- and middle-income countries (LMICs). In this study, we report a functional, transferable, plasmid-mediated mcr-1 gene in S. flexneri. We have shown that mcr-1 is located on a novel composite transposon which is flanked by inverted repeats of ISApl1. The host strain is multidrug resistant, and this multidrug resistance is also transferable. The finding of a functional mcr-1 gene in S. flexneri, a human-associated Enterobacteriaceae family member, is a cause for concern as infections due to S. flexneri are the main Shigella infections in most low- and middle-income countries.
Antimicrobial activity of Calophyllum inophyllum crude extracts obtained by pressurized liquid extraction

The fruit peel of Calophyllum inophyllum is considered waste material from the production of oils from its fruit and is abundantly available in Vietnam. The preparation of extracts was carried out by the pressurized liquid extraction (PLE) method. The preliminary phytochemical screening revealed the presence of phenolic compounds. The antimicrobial studies of the methanolic and n-hexane extracts were carried out on standard micro-organisms, Staphylococcus aureus (ATCC 6538 P), Mycobacterium smegmatis (ATCC 14468), and Pseudomonas aeruginosa (ATCC 9027), using the disc diffusion method. The extracts demonstrated promising antibacterial activity against Staphylococcus aureus and Mycobacterium smegmatis. The presence of phenolic compounds was likely to be responsible for these activities.
Complementation of the Mycoplasma synoviae MS-H vaccine strain with wild-type obg influencing its growth characteristics

The temperature-sensitive (ts+) Mycoplasma synoviae vaccine strain MS-H harbors a non-synonymous mutation which results in Glycine to Arginine substitution at position 123 in the highly conserved glycine-rich motif of Obg-fold in the GTP-binding protein Obg. In-silico analysis of the wild-type and mutant Obgs of M. synoviae has indicated that this amino acid substitution affects structure of the protein, potentially leading to abrogation of Obg function in vivo. Present study was conducted to develop the first expression vector for M. synoviae and to investigate the potential effect(s) of complementation of MS-H vaccine with the wild-type obg from 86079/7NS, the parent strain of MS-H. An oriC vector, pKS-VOTL, harboring the 86079/7NS obg gene, downstream of the variable lipoprotein haemagglutinin (vlhA) gene promoter, also cloned from 86079/7NS, was used to transform MS-H. The plasmid was localised at the chromosomal oriC locus of MS-H without any detectable integration at the chromosomal obg locus. Analysis of the MS-H transformants revealed abundant obg transcripts as well as Obg protein, when compared to the MS-H transformed with a similar vector, pMAS-LoriC, lacking obg coding sequence. The MS-H transformants complemented with wild-type Obg maintained their original temperature-sensitivity phenotype (consistent with MS-H vaccine) but, when compared to the MS-H transformed with pMAS-LoriC, had significantly higher (p < 0.05) growth rate and viability at the permissive (33°C) and non-permissive temperature (39.5°C), respectively. Analysis of Obg expression in MS-H and its wild-type parent strain revealed comparatively lower levels of Obg in MS-H. These results indicate that not only the mutation in Obg, but also the level of Obg expression, can confer functional abnormalities in the bacterial host. Furthermore, with the construction of first expression vector for M. synoviae, this study has set foundation for the development of recombinant vaccine(s) based on MS-H.
RTS Noise Characterization in Single-Photon Avalanche Diodes

Random telegraph signal (RTS) behavior is reported and characterized in the dark count rate of single-photon avalanche Diodes (SPADs). The RTS is observed in a SPAD fabricated in 0.8-μm CMOS technology and in four proton-irradiated SPADs designed and fabricated in 0.35-μm CMOS technology. The RTS characteristics are evaluated experimentally and verified theoretically with respect to bias and temperature.
On the Estimation of Complex Speech DFT Coefficients Without Assuming Independent Real and Imaginary Parts

This letter considers the estimation of speech signals contaminated by additive noise in the discrete Fourier transform (DFT) domain. Existing complex-DFT estimators assume independency of the real and imaginary parts of the speech DFT coefficients, although this is not in line with measurements. In this letter, we derive some general results on these estimators, under more realistic assumptions. Assuming that speech and noise are independent, speech DFT coefficients have uniform phase, and that noise DFT coefficients have a Gaussian density, we show theoretically that the spectral gain function for speech DFT estimation is real and upper-bounded by the corresponding gain function for spectral magnitude estimation. We also show that the minimum mean-square error (MMSE) estimator of the speech phase equals the noisy phase. No assumptions are made about the distribution of the speech spectral magnitudes. Recently, speech spectral amplitude estimators have been derived under a generalized-Gamma amplitude distribution. As an example, we will derive the corresponding complex-DFT estimators, without making the independence assumption.
Adult Intussusception

Adult intussusception is rare. We report the case of an elderly female patient with an ileocecal intussusception who underwent resection and ileocolic anastomosis. The histology revealed chronic inflammation of the ileum and cecum and there was no evidence of malignancy. There was no evidence of malignancy. The appendix showed fibrous obliteration of the lumen.
A placebo-controlled 18-month trial of lamotrigine and lithium maintenance treatment in recently manic or hypomanic patients with bipolar I disorder.

BACKGROUND Lamotrigine has been shown to be an effective treatment for bipolar depression and rapid cycling in placebo-controlled clinical trials. This double-blind, placebo-controlled study was conducted to assess the efficacy and tolerability of lamotrigine and lithium compared with placebo for the prevention of relapse or recurrence of mood episodes in recently manic or hypomanic patients with bipolar I disorder. METHODS After an 8- to 16-week open-label phase during which treatment with lamotrigine was initiated and other psychotropic drug regimens were discontinued, patients were randomized to lamotrigine (100-400 mg daily), lithium (0.8-1.1 mEq/L), or placebo as double-blind maintenance treatment for as long as 18 months. RESULTS Of 349 patients who met screening criteria and entered the open-label phase, 175 met stabilization criteria and were randomized to double-blind maintenance treatment (lamotrigine, 59 patients; lithium, 46 patients; and placebo, 70 patients). Both lamotrigine and lithium were superior to placebo at prolonging the time to intervention for any mood episode (lamotrigine vs placebo, P =.02; lithium vs placebo, P =.006). Lamotrigine was superior to placebo at prolonging the time to a depressive episode (P =.02). Lithium was superior to placebo at prolonging the time to a manic, hypomanic, or mixed episode (P =.006). The most common adverse event reported for lamotrigine was headache. CONCLUSIONS Both lamotrigine and lithium were superior to placebo for the prevention of relapse or recurrence of mood episodes in patients with bipolar I disorder who had recently experienced a manic or hypomanic episode. The results indicate that lamotrigine is an effective, well-tolerated maintenance treatment for bipolar disorder, particularly for prophylaxis of depression.