Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational methods for ribosome profiling data analysis

Since the introduction of the ribosome profiling technique in 2009 its popularity has greatly increased. It is widely used for the comprehensive assessment of gene expression and for studying the mechanisms of regulation at the translational level. As the number of ribosome profiling datasets being produced continues to grow, so too does the need for reliable software that can provide answers to the biological questions it can address. This review describes the computational methods and tools that have been developed to analyze ribosome profiling data at the different stages of the process. It starts with initial routine processing of raw data and follows with more specific tasks such as the identification of translated open reading frames, differential gene expression analysis, or evaluation of local or global codon decoding rates. The review pinpoints challenges associated with each step and explains the ways in which they are currently addressed. In addition it provides a comprehensive, albeit incomplete, list of publicly available software applicable to each step, which may be a beneficial starting point to those unexposed to ribosome profiling analysis. The outline of current challenges in ribosome profiling data analysis may inspire computational biologists to search for novel, potentially superior, solutions that will improve and expand the bioinformatician's toolbox for ribosome profiling data analysis.
Safety and cost of drug‐induced sleep endoscopy outside the operating room

Drug‐induced sleep endoscopy (DISE) is used to assess site of obstruction for patients in a pharmacologically induced sleep‐like state. It is traditionally performed in the operating room (OR), however, no data exists regarding the feasibility of this intervention outside the OR in children. The objective is to compare the safety of DISE performed in the MRI induction room to those performed in the OR.
A systematic review protocol

Background: Pelvic organ prolapse (POP) is the downward descent of vaginal walls, affecting the health of 32% to 76% female patients. Conservative interventions are considered as priority before seeking help from surgery. We plan to make the systematic review to assess the effectiveness of conservative intervention for adult women with POP. Methods:Studies will be searched in PubMed, EMBASE, and the Cochrane Library from inception to July 2017. Primary outcomes are specific POP-related symptom, severity of prolapse, Prolapse-related, and general health-related quality of life and other nonPOP-specific symptoms. Results: The data will be synthesized if possible using MD, SMD or RR. A descriptive analysis will be made if the data cannot be synthesized. Discussion: The systematic review might provide solid evidence for the treatment of POP by conservative intervention. Abbreviations: POP= pelvic organ prolapse, PRISMA-P= Preferred Reporting Items for Systematic Reviews andMeta-Analyses protocols.
Even-number Measurement Bias with Goldmann Applanation Tonometry.

While working with a large dataset of Goldmann applanation tonometry (GAT) intraocular pressure (IOP) measurements for a separate investigation, we observed that the IOP distribution favored even-numbered values. Study of this phenomenon has been limited, and this larger dataset enabled inquiry that showed new insight concerning the manner in which this bias may vary according to IOP level. This analysis of 69,537 right eyes measured via GAT demonstrated that even-number preference was essentially absent in the 21-24▒mm Hg range, but then the bias gradually strengthened as it moved away from this range in a lower or higher IOP direction. These data suggest that there is an examiner proclivity to measure and/or record GAT readings as even-numbered values, but that this tendency varies depending on IOP level.
Left ventricular diastolic dysfunction in HIV-uninfected infants exposed in utero to antiretroviral therapy.

OBJECTIVES To longitudinally measure LV diastolic function in HIV-exposed but uninfected (HEU) children perinatally-exposed to ART. DESIGN HEU children who were perinatally-exposed to antiretroviral therapy (ART) may be at risk for adverse cardiac effects. We have previously reported that those children have decreased left ventricular (LV) mass, dimension, and septal thickness with increased contractility. METHODS Serial echocardiograms were obtained at specific times from birth to 48 months from two groups of HIV-uninfected children: 148 HIV-negative children who were perinatally-exposed to ART and 130 non-ART-exposed HIV-unexposed healthy controls. The following LV diastolic indices were obtained: mitral valve early and late diastolic velocity (E and A), tissue Doppler derived LV free wall and septal early diastolic velocity (LVe' and sep e'). RESULTS All echocardiographic indices were significantly different in ART-exposed children compared to ART-unexposed healthy controls. Both E and A were overall lower at all ages by 8.28 cm/sec (P = 0.0002) and 13.46 cm/sec (P < 0.0001) respectively. E/A ratio was higher by 0.27, 0.46, and 0.28 units at birth, 1 year and 2 years of age, respectively (all P ≤ 0.01). Moreover, LVe' and sep e' were overall lower at all ages by 0.84 cm/sec (P = 0.01) and 0.47 cm/sec (P = 0.02) respectively. CONCLUSIONS Children who were exposed to ART in utero have subclinical yet significant differences in specific LV diastolic indices. Follow-up with serial echocardiograms is recommended in this population to further assess the potential cardiac toxicity of perinatal exposure to ART.
Assessment of DNA Susceptibility to Denaturation as a Marker of Chromatin Structure

The susceptibility of DNA in situ to denaturation is modulated by its interactions with histone and nonhistone proteins, as well as with other chromatin components related to the maintenance of the 3D nuclear structure. Measurement of DNA proclivity to denature by cytometry provides insight into chromatin structure and thus can be used to recognize cells in different phases of the cell cycle, including mitosis, quiescence (G0), and apoptosis, as well as to identify the effects of drugs that modify chromatin structure. Particularly useful is the method's ability to detect chromatin changes in sperm cells related to DNA fragmentation and infertility. This article presents a flow cytometric procedure for assessing DNA denaturation based on application of the metachromatic property of acridine orange (AO) to differentially stain single‐ versus double‐stranded DNA. This approach circumvents limitations of biochemical methods of examining DNA denaturation, in particular the fact that the latter destroy higher orders of chromatin structure and that, being applied to bulk cell populations, they cannot detect heterogeneity of individual cells. Because the metachromatic properties of AO have also found application in other cytometric procedures, such as differential staining of RNA versus DNA and assessment of lysosomal proton pump including autophagy, to avert confusion between these approaches and the use of this dye in the DNA denaturation assay, these AO applications are briefly outlined in this unit as well. © 2019 by John Wiley & Sons, Inc.
Qualitative Contributions to Implementation Research on HIV Prevention and Treatment.

BACKGROUND The advantages of conducting implementation research as part of the development, as well as delivery and use of HIV prevention and treatment interventions, are increasingly being recognized. Qualitative methods are gaining recognition in implementation-oriented research on HIV as vehicles for examining particular implementation outcomes and for identifying barriers and facilitators to intervention uptake. However, they have more to offer. This article presents 3 case examples illustrating the use of qualitative research to explain intervention processes and outcomes, with the goal of clarifying "how and why" they work. METHODS/CASE EXAMPLES The first example identifies active ingredients in an intervention aimed at improving antiretroviral therapy (ART) adherence. The second proposes an explanation of the processes through which community-based HIV testing with follow-up support may bring about linkage to care and prevention services. The third unpacks the dynamics of a novel strategy of delivering oral pre-exposure prophylaxis and ART to HIV serodiscordant couples, showing how the organization of services positively impacted participating couples, enabling them to use oral pre-exposure prophylaxis and ART effectively to prevent HIV transmission. RESULTS/DISCUSSION Qualitative methods contribute to implementation research for HIV intervention development by (1) offering an alternative to framework-driven investigation, (2) providing tools for understanding user experience of interventions, and (3) developing local explanations of intervention processes and outcomes. CONCLUSION In various ways, qualitative methods contribute to implementation research by deepening and "thickening" conceptualization of implementation problems. Stronger conceptualizations lead to stronger implementation strategies and, thus, to increased use of evidence-based interventions for HIV prevention and treatment as they are made available to the public worldwide.
In situ pH measurements of individual levitated microdroplets using aerosol optical tweezers.

The pH of microscale reaction environments controls numerous physicochemical processes, requiring a real-time pH micro-probe. We present highly accurate real-time pH measurements of microdroplets using aerosol optical tweezers (AOT) and analysis of the Whispering Gallery Modes (WGMs) contained in the cavity-enhanced Raman spectra. Uncertainties ranging from ±0.03 to 0.06 in pH for picoliter droplets are obtained through averaging Raman frames acquired at 0.5 Hz over 3.3 minutes. The high accuracy in pH determination is achieved by combining two independent measurements uniquely provided by the AOT approach: the anion concentration ratio from the spontaneous Raman spectra, and the total solute concentration from the refractive index retrieved from WGM analysis of the stimulated cavity-enhanced Raman spectra. pH can be determined over a range of -0.36 to 0.76 using the aqueous sodium bisulfate system. This technique enables direct measurements of pH-dependent chemical and physical changes experienced by individual microparticles, and exploration of the role of pH in the chemical behavior of confined microenvironments.
Combined test of third lumbar skeletal muscle index and prognostic nutrition index improve prognosis prediction power in resected colorectal cancer liver metastasis

Background: In this paper, we aim to explore clinical value of skeletal muscle index (SMI) and prognostic nutrition index (PNI) on resected colorectal cancer liver metastasis (CRLM). Results: Among the 539 patients, 355 were males. Baseline lower SMI was associated with smaller BMI, smaller PNI, smaller pre-albumin and longer hospitalization days (P<0.05). Patients with lower SMI and PNI had significantly shorter duration of PFS and OS (P<0.05). SMI can reflect the postoperative treatment response. Postoperative 6-month’s and 12-month’s SMI and PNI can indicate overall prognosis. When combined SMI and PNI, prognostic AUC of ROC curves improved significantly. Conclusion: Combined monitor of SMI and PNI can improve the power at predicting prognosis. Postoperative 6-month’s record of SMI and PNI was more accurate and predictive for CRLM prognosis. Method: A total of 539 resected CRLM patients between January 2013 to December 2016 with complete clinical data were included. Computed tomography image was collected from each patient. Receiver-operating characteristic (ROC) curves were constructed; area under curves (AUC) were also determined. All clinical variables were analyzed in proper way.
Computational and Biological Methods for Gene Therapy.

With the rapid development of sequencing technologies, it is more efficient to reveal the variations and expression levels of molecules in the genome, transcriptome, and proteome, which have greatly helped to expose the risk factors of human diseases. To achieve the goal, in addition to the biological research of the wet laboratory, more knowledge needs to be mined from a large amount of sequencing data. To this end, bioinformatics methods have been introduced to help researchers identify more etiological genes, biomarkers associated with clinical molecular subtypes and prognosis. Whereas, most of the methods focus on analyzing single omics data, only providing a partial reference to human diseases. Therefore, the major challenge is how to mine novel causal genes and phenotypes of diseases based on the fusing multi-level omics data using system biology approaches, improving the efficacy of gene therapy. Here, a Special Issue of Current Gene Therapy around the topic Computational and Biological Methods for Gene Therapy is proposed. In total, five outstanding works were presented in this thematic issue.
Separation of Bromoalkanes Isomers by Nonporous Adaptive Crystals of Leaning Pillar[6]arene.

Haloalkanes are important chemicals in synthetic chemistry and petrochemical industry, but the separation of their isomers is a big hurdle. Here we report a facile energy-efficient adsorptive separation strategy using a new class of nonporous adaptive crystals based on leaning pillar[6]arene. Desolvated perethylated leaning pillar[6]arene crystals (EtLP6) with interesting nonporous character show a preference for 1-bromoalkane isomers over 2-bromoalkane isomers. EtLP6 is capable of separating 1-bromopropane, 1-bromobutane, and 1-bromopentane from the corresponding 1:1 (v/v) mixtures of 1/2-positional isomers with purities from 89.6% to 96.3% in only one adsorption cycle. Single-crystal structure analysis in conjunction with powder X-ray diffraction patterns and thermoanalysis suggest that the selectivity is endowed by the different host-guest binding modes and different stabilities of EtLP6 crystalloids loaded with 1- and 2-positional isomers. Significantly, the guest-adsorbed assemblies are highly stable at room temperature and EtLP6 can be reused many times without any decrease in performance.
Preliminary investigation of the effect of treating sheep during pregnancy with a vitamin A, D, E formulation on the incidence of vaginal prolapse

ABSTRACT Aim: To determine if vitamin D3 treatment reduced the incidence of vaginal prolapse in pregnant sheep on a North Canterbury sheep breeding property. Methods: Pregnant ewes from a single farm were allocated to three treatment groups in May 2018. At this time, the first group (EarlyVitADE; n = 512) received an I/M 1 mL dose of 500,000 IU/mL vitamin D3, 60,000 IU/mL vitamin A, and 25 mg/mL vitamin E. This was repeated in July 2018, when the second group (LateVitADE; n = 695) also received the same treatment. The third group (n = 737) were untreated controls. All cases of vaginal prolapse on the property were recorded from pregnancy diagnosis in June 2018 until ewes were set-stocked in August 2018. The planned start of lambing was 10 August 2018. Results: During the period of observation, vaginal prolapses were recorded in 3/699 (0.4%) 2-year-old ewes, and the odds of vaginal prolapse were not associated with treatment group in these ewes (p > 0.3). Amongst ewes aged ≥3 years, during the same period, there were 6/333 (1.8%), 6/443 (1.4%) and 25/469 (5.3%) cases in the EarlyVitADE, LateVitADE and control groups, respectively. Compared to control ewes, the odds of vaginal prolapse were reduced in both the EarlyVitADE (OR = 0.37; 95% CI = 0.15–0.92) and LateVitADE (OR = 0.25; 95% CI = 0.10–0.62) treatment groups. Conclusions and clinical relevance: In this preliminary study, administration of injectable vitamins A, D3, and E to pregnant ewes reduced the incidence of vaginal prolapse during the period from pregnancy diagnosis to set-stocking on one North Canterbury hill-country farm. Due to the restricted data collection period, this investigation should be replicated to better quantify the repeatability of the observed treatment effect over the complete lambing period.
Damage control: Differentiating incontinence-associated dermatitis from pressure injury.

Skin injuries such as incontinenceassociated dermatitis (IAD) and pressure injuries are increasingly monitored and benchmarked as a quality indicator for hospitals and nursing facilities. Pressure injuries are documented by Medicare and Medicaid-certifi ed skilled nursing facilities in the Minimum Data Set, and pressure injury incidence rates are publicly reported as a quality measure in the Nursing Home Compare website. Many clinicians have diffi culty distinguishing superfi cial skin injuries from early-stage pressure injuries because the differences can be very subtle. Mistaking IAD for an earlystage pressure injury can result in ineffective treatment and possible deterioration to full-thickness injury. This is particularly true in patients with dark skin tones because visual cues associated with these types of skin injuries may not be easy to detect. Likewise, failure to detect blanchable and nonblanchable erythema in a patient with dark skin tones may increase the patient’s risk of developing a full-thickness skin injury. This article discusses how to differentiate, classify, and document IAD and pressure injuries with an emphasis on assessing patients with dark skin. ■ Correct assessment is critical Accurate classifi cation of skin injuries and identifi cation of their etiology is essential to ensure that the correct treatment plan is initiated to halt the injury and support healing. Besides impacting patient care, inaccurate identifi cation of skin injuries can negatively affect benchmarking data and payments to the facility. Many clinicians have diffi culty making the correct identifi cation because these injuries can have very subtle differences. Pressure injuries have traditionally been classifi ed using a staging system based on depth of tissue injury. These have been revised over the years to incorporate the current understanding of the science of pressure injury pathology and etiology (see NPUAP pressure injury stages). Full discussion and description of all pressure injury stages is beyond the scope of this article, but additional information can be accessed from the National Pressure Ulcer Advisory Panel (NPUAP) website at www.npuap. org/resources/educationaland-clinical-resources/npuappressure-injury-stages. The NPUAP staging system should be used only for injuries caused by pressure. Other skin injuries can be classifi ed as either fullthickness or partial-thickness, depending on the depth of tissue damage in the wound. This discussion focuses on Stage 1 and 2 pressure injuries and Deep Tissue Pressure Injuries (DTPI) as defi ned by the NPUAP because these are the pressure injuries most likely to be confused with IAD. The diffi culty in differentiating Stage 1, Stage 2, or suspected DTPI from IAD has been documented in the literature as problematic, particularly in patients with dark skin. Improving the clinician ability to correctly identify skin injuries can lead to better patient outcomes.
Relationship Between Foveal Threshold and Macular Structure/Function/Vessel Density in Glaucoma

Purpose: To investigate the hypothesis that macular structure, function, and vessel density (VD) measurements can predict foveal threshold (FT) outcomes in glaucomatous eyes. Materials and Methods: One hundred ninety-five eyes from 195 subjects (134 subjects with early-to-moderate stage open-angle glaucoma and 61 healthy controls) who underwent optical coherence tomography angiography imaging and 24-2 visual field (VF) testing with FT measurements on the same day were retrospectively enrolled in this study. The association of FT with macular structural/functional/VD measurements was evaluated using partial correlation analyses with adjustment for age and linear regression analyses. Results: FT showed significant correlations between the thickness of the macular ganglion cell-inner plexiform layer (mGCIPL) (r=0.330, P<0.001) and the mean sensitivity (MS) of the central 5 and 10 degrees VF points (r=0.448, P<0.001 and r=0.361, P<0.001). Significant correlations were also found between FT and VD measurements at the inferior and superior parafoveal sectors (r=0.455, P<0.001 and r=0.438, P<0.001). In multivariate linear regression analyses controlling the covariates, the thickness of the mGCIPL, central 5 degrees VF MS, and parafoveal VD were significantly associated with FT (all P<0.001). There was also a significant association between FT and logMAR best-corrected visual acuity (β=−5.647, P<0.001). Conclusions: Macular VD along with mGCIPL thickness and central 5 degrees VF MS independently predict FT outcomes even in the eyes of patients with early-to-moderate stage open-angle glaucoma.
SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes

MOTIVATION Whole genome sequencing of uncultured eukaryotic genomes is complicated by difficulties in acquiring sufficient amounts of tissue. Single cell genomics (SCG) by multiple displacement amplification (MDA) provides a technical workaround, yielding whole genome libraries which can be assembled de novo. Downsides of MDA include coverage biases and exacerbation of contamination. These factors affect assembly continuity and fidelity, complicating discrimination of genomes from contamination and noise by available tools. Uncultured eukaryotes and their relatives are often underrepresented in large sequence data repositories, further impairing identification and separation. RESULTS We compare the ability of filtering approaches to remove contamination and resolve eukaryotic draft genomes from SCG metagenomes, finding significant variation in outcomes. To address these inconsistencies, we introduce a consensus approach that is codified in the SCGid software package. SCGid parallelly filters assemblies using different approaches, yielding three intermediate drafts from which consensus is drawn. Using genuine and mock SCG metagenomes, we show that our approach corrects for variation among draft genomes predicted by individual approaches and outperforms them in recapitulating published drafts in a fast and repeatable way, providing a useful alternative to available methods and manual curation. AVAILABILITY AND IMPLEMENTATION The SCGid package is implemented in python2 and R. Source code is available at http://www.github. com/amsesk/SCGid under the GNU GPL 3.0 license. SUPPLEMENTARY INFORMATION Supplementary information is available at Bioinformatics online.
Development, validation and reliability of the Chrononutrition Profile - Questionnaire

ABSTRACT Chrononutrition, or the circadian timing of food intake, has garnered attention as a topic of study due to its associations with health (e.g. weight gain); however, a valid and reliable assessment of chrononutrition in daily life has not yet been developed. This paper details the development and initial reliability and validity testing of the Chrononutrition Profile – Questionnaire (CP-Q). The CP-Q assesses six components of chrononutrition that are likely to influence health (breakfast skipping, largest meal, evening eating, evening latency, night eating, and eating window). This questionnaire is designed to assess general chrononutrition behaviors and preferred timing of food intake. The CP-Q can be used as a sole evaluation of chrononutrition, and can also be utilized in conjunction with existing dietary measures to provide a comprehensive assessment of one’s eating behaviors. This measure offers health-care professionals, researchers, and stakeholders a cost-effective and comprehensive method of evaluating chrononutrition and identifying targets for health improvement.