Discovering unknown human and mouse transcription factor binding sites and their characteristics from ChIP-seq data.

Transcription factor binding sites (TFBSs) are essential for gene regulation, but the number of known TFBSs remains limited. We aimed to discover and characterize unknown TFBSs by developing a computational pipeline for analyzing ChIP-seq (chromatin immunoprecipitation followed by sequencing) data. Applying it to the latest ENCODE ChIP-seq data for human and mouse, we found that using the irreproducible discovery rate as a quality-control criterion resulted in many experiments being unnecessarily discarded. By contrast, the number of motif occurrences in ChIP-seq peak regions provides a highly effective criterion, which is reliable even if supported by only one experimental replicate. In total, we obtained 2,058 motifs from 1,089 experiments for 354 human TFs and 163 motifs from 101 experiments for 34 mouse TFs. Among these motifs, 487 have not previously been reported. Mapping the canonical motifs to the human genome reveals a high TFBS density ±2 kb around transcription start sites (TSSs) with a peak at -50 bp. On average, a promoter contains 5.7 TFBSs. However, 70% of TFBSs are in introns (41%) and intergenic regions (29%), whereas only 12% are in promoters (-1 kb to +100 bp from TSSs). Notably, some TFs (e.g., CTCF, JUN, JUNB, and NFE2) have motifs enriched in intergenic regions, including enhancers. We inferred 142 cobinding TF pairs and 186 (including 115 completely) tethered binding TF pairs, indicating frequent interactions between TFs and a higher frequency of tethered binding than cobinding. This study provides a large number of previously undocumented motifs and insights into the biological and genomic features of TFBSs.

Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2.

SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2-S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates.

Effectiveness of Sodium Bicarbonate Administration on Mortality in Cardiac Arrest Patients: A Systematic Review and Meta-analysis.

BACKGROUND: The 2010 Advanced Cardiac Life Support guidelines stated that routine sodium bicarbonate (SB) use for cardiac arrest patients was not recommended. However, SB administration during resuscitation is still common. OBJECTIVES: To evaluate the effect of SB on return of spontaneous circulation (ROSC) and survival-to-discharge rates in adult cardiac arrest patients. METHODS: We searched Medline, Scopus, and Cochrane Central Register of Controlled Trials (CENTRAL) from inception to December 2019. We included trials on nontraumatic adult patients after cardiac resuscitation and SB treatment vs. controls. RESULTS: A meta-analysis was performed with six observational studies, including 18,406 adult cardiac arrest patients. There were no significant differences in the ROSC rate (odds ratio [OR] 1.185; 95% confidence interval [CI] 0.680-2.065) and survival-to-discharge rate (OR 0.296; 95% CI 0.066-1.323) between the SB and no-SB groups. In the subgroup analysis based on the year factor, there were no significant differences in the mortality rate in the After-2010 group. In the subgroup analysis based on the continent, the ROSC rate (OR 0.521; 95% CI 0.432-0.628) and survival-to-discharge rate (OR 0.102; 95% CI 0.066-0.156) were significantly lower in the North American group. CONCLUSIONS: SB use was not associated with improvement in ROSC or survival-to-discharge rates in cardiac resuscitation. In addition, mortality was significantly increased in the North American group with SB administration.

SURGICAL OUTCOMES IN EYES WITH EXTREMELY HIGH MYOPIA FOR MACULAR HOLE WITHOUT RETINAL DETACHMENT.

PURPOSE: The authors evaluated surgical outcomes in eyes with extremely high myopia for macular hole (MH) without retinal detachment. METHODS: In this retrospective study, 14 eyes with axial lengths of ≥30.0 mm underwent vitrectomy and internal limiting membrane (ILM) peeling with or without inverted ILM flap insertion for MH without retinal detachment (October 2009-June 2016). Outcome measures were MH closure confirmed by optical coherence tomography, best-corrected visual acuity, and complications. RESULTS: The mean axial length was 30.69 ± 0.76 mm. The overall final closure rate was 85.7% (12/14 eyes); the mean follow-up was 17.29 (±20.20) months. Primary anatomical MH closure after 1 operation was achieved in three of eight eyes (37.5%) without an inverted ILM flap and was achieved in six of six eyes (100%) with inverted ILM flap insertion (P = 0.031). There was no reopening of MH during follow-up. Mean visual acuity improved significantly from 1.10 ± 0.43 logarithm of the minimum angle of resolution (Snellen equivalent, 20/254) to 0.84 ± 0.50 logarithm of the minimum angle of resolution (Snellen equivalent, 20/138) (P = 0.046; 2-tailed, paired t-test). Only 1 eye developed an MH-associated retinal detachment 4.5 years after previously failed MH surgery; reattachment was achieved after a second operation. CONCLUSION: Patients with extremely high myopia obtained anatomical and functional improvements from MH surgery; inverted ILM flap insertion achieved significantly higher primary success rates in MH closure.

Choroidal Neovascularization Secondary to Intense Pulsed Light Injury.

The authors report a 26-year-old medical device saleswoman developing choroidal neovascularization after injury by intense pulsed light with detection and monitoring by optical coherence tomography angiography and treatment with intravitreal injection of ranibizumab. This is the first intense pulsed light-related choroidal neovascularization case, which reminds the importance of using appropriate eye protection throughout the course of treatment for all individuals present in the therapy room.

A WHEP Domain Regulates the Dynamic Structure and Activity of Caenorhabditis elegans Glycyl-tRNA Synthetase.

WHEP domains exist in certain eukaryotic aminoacyl-tRNA synthetases and play roles in tRNA or protein binding. We present evidence herein that cytoplasmic and mitochondrial forms of Caenorhabditis elegans glycyl-tRNA synthetase (CeGlyRS) are encoded by the same gene (CeGRS1) through alternative initiation of translation. The cytoplasmic form possessed an N-terminal WHEP domain, whereas its mitochondrial isoform possessed an extra N-terminal sequence consisting of an mitochondrial targeting signal and an appended domain. Cross-species complementation assays showed that CeGRS1 effectively rescued the cytoplasmic and mitochondrial defects of a yeast GRS1 knock-out strain. Although both forms of CeGlyRS efficiently charged the cytoplasmic tRNAs(Gly) of C. elegans, the mitochondrial form was much more efficient than its cytoplasmic counterpart in charging the mitochondrial tRNA(Gly) isoacceptor, which carries a defective TψC hairpin. Despite the WHEP domain per se lacking tRNA binding activity, deletion of this domain reduced the catalytic efficiency of the enzyme. Most interestingly, the deletion mutant possessed a higher thermal stability and a somewhat lower structural flexibility. Our study suggests a role for the WHEP domain as a regulator of the dynamic structure and activity of the enzyme.

Modulating the Structure and Function of an Aminoacyl-tRNA Synthetase Cofactor by Biotinylation.

Arc1p is a yeast-specific tRNA-binding protein that forms a ternary complex with glutamyl-tRNA synthetase (GluRSc) and methionyl-tRNA synthetase (MetRS) in the cytoplasm to regulate their catalytic activities and subcellular distributions. Despite Arc1p not being involved in any known biotin-dependent reaction, it is a natural target of biotin modification. Results presented herein show that biotin modification had no obvious effect on the growth-supporting activity, subcellular distribution, tRNA binding, or interactions of Arc1p with GluRSc and MetRS. Nevertheless, biotinylation of Arc1p was temperature dependent; raising the growth temperature from 30 to 37 °C drastically reduced its biotinylation level. As a result, Arc1p purified from a yeast culture that had been grown overnight at 37 °C was essentially biotin free. Non-biotinylated Arc1p was more heat stable, more flexible in structure, and more effective than its biotinylated counterpart in promoting glutamylation activity of the otherwise inactive GluRSc at 37 °C in vitro Our study suggests that the structure and function of Arc1p can be modulated via biotinylation in response to temperature changes.

Study on the Effects of Quantum Well Location on Optical Characteristics of AlGaN/GaN Light-Emitting HEMT.

In this study, AlGaN/GaN light-emitting HEMTs (LE-HEMT) with a single quantum well inserted in different locations in the epitaxy layers are fabricated and analyzed. For both structures, light-emitting originated from electrons in the 2DEG and holes from the p-GaN for radiative recombination is located in the quantum well. To investigate the importance of the location of single quantum well, optical characteristics are compared by simulation and experimental results. The experimental results show that the main light-emitting wavelength is shifted from 365 nm in the UV range to 525 nm in the visible range when the radiative recombination is confined in the quantum well and dominates among other mechanisms. Epi B, which has a quantum well above the AlGaN barrier layer in contrast to Epi A which has a quantum well underneath the barrier, shows better intensity and uniformity in light-emitting. According to the simulation results showing the radiative distribution and electron concentrations for both structures, the lower quantum efficiency is due to the diverse current paths in Epi A. On the other hand, Epi B shows better quantum confinement and therefore better luminescence in the same bias condition, which is consistent with experimental observations. These findings are critical for advancing the performance of LE-HEMTs.

In-hospital mortality associated with necrotizing soft tissue infection due to Vibrio vulnificus: a matched-pair cohort study.

BACKGROUND: It remains unclear whether Vibrio vulnificus necrotizing soft tissue infection (NSTI) is associated with higher mortality compared with non-Vibrio NSTI. This study's objective was to compare outcomes including in-hospital mortality and prognosis between patients with V. vulnificus NSTI and those with non-Vibrio NSTI. METHOD: A retrospective 1:2 matched-pair cohort study of hospitalized patients with NSTI diagnosed by surgical finding was conducted in two tertiary hospitals in southern Taiwan between January 2015 and January 2020. In-hospital outcomes (mortality, length of stay) were compared between patients with and without V. vulnificus infection. We performed multiple imputation using chained equations followed by multivariable regression analyses fitted with generalized estimating equations to account for clustering within matched pairs. All-cause in-hospital mortality and length of stay during hospitalization were compared for NSTI patients with and without V. vulnificus. RESULT: A total of 135 patients were included, 45 in V. vulnificus NSTI group and 90 in non-Vibrio group. The V. vulnificus NSTI patients had higher mortality and longer hospital stays. Multivariable logistic regression analysis revealed that V. vulnificus NSTI was significantly associated with higher in-hospital mortality compared with non-Vibrio NSTI (adjusted odds ratio = 1.52; 95% confidence interval 1.36-1.70; p < 0.01). CONCLUSION: Vibrio vulnificus NSTI was associated with higher in-hospital mortality and longer hospital stay which may increase health care costs, suggesting that preventing V. vulnificus infection is essential.

Differentiating necrotizing soft tissue infections from cellulitis by soft tissue infectious fluid analysis: a pilot study.

BACKGROUND: We conducted this study to evaluate the characteristics of the infectious fluid in soft tissue infection and investigate the utility of the biochemical tests and Gram stain smear of the infectious fluid in distinguishing necrotizing soft tissue infection (NSTI) from cellulitis. METHODS: This retrospective cohort study was conducted in a tertiary care hospital in Taiwan. From April 2019 to October 2020, patients who were clinically suspected of NSTI with infectious fluid accumulation along the deep fascia and received successful ultrasound-guided aspiration were enrolled. Based on the final discharge diagnosis, the patients were divided into NSTI group, which was supported by the surgical pathology report, or cellulitis group. The t test method and Fisher's exact test were used to compare the difference between two groups. The receiver-operator characteristic (ROC) curves and area under the ROC curve (AUC) were used to evaluate the discriminating ability. RESULTS: Total twenty-five patients were enrolled, with 13 patients in NSTI group and 12 patients in cellulitis group. The statistical analysis showed lactate in fluid (AUC = 0.937) and LDH in fluid (AUC = 0.929) had outstanding discrimination. The optimal cut-off value of fluid in lactate was 69.6 mg/dL with corresponding sensitivity of 100% and specificity of 76.9%. The optimal cut-off value of fluid in LDH was 566 U/L with corresponding sensitivity of 83.3% and a specificity of 92.3%. In addition, albumin in fluid (AUC = 0.821), TP in fluid (AUC = 0.878) and pH in fluid (AUC = 0.858) also had excellent diagnostic accuracy for NSTI. The Gram stain smear revealed 50% bacteria present in NSTI group and all the following infectious fluid culture showed bacteria growth. CONCLUSIONS: The analysis of infectious fluid along the deep fascia might provide high diagnostic accuracy to differentiate NSTI from cellulitis.

Micellar transitions in solvent-annealed thin films of an amphiphilic block copolymer controlled with tunable surface fields.

We investigated the response of symmetric poly(styrene-block-4vinylpyridine) P(S-b-4VP) diblock copolymer micelles to surface fields of variable strength at free surfaces and substrate interfaces when the micelles as spun were subjected to solvent annealing. Free surface interactions were controlled with solvent annealing in solvents of varied selectivity. On exposure to vapors of a solvent strongly selective for PS, the micelles retained their spherical shape but grew into cylindrical micelles or lamellar nanostructures via fusion on exposure to slightly selective or neutral solvent vapors. Giant 2D disks that completely wetted PS-grafted substrates resulted when spherical micelles were exposed to vapors of a highly selective solvent for P4VP. The interfacial interactions were controlled through subjecting them to UV/ozone (UVO) substrates initially coated with an end-grafted layer of short PS chains, with which the grafted PS chains became oxidized, degraded, or totally removed through UVO treatment for a controlled duration. When thin films were annealed in vapors of THF, the structural transition from spherical to cylindrical micelles depended on the interfacial field. On applying selective UVO exposure of optimal duration, we fabricated a substrate with two interfacial chemistries that promoted varied micellar species (spherical and cylindrical micelles) with a sharp boundary developed within thin films through solvent annealing for a controlled duration.

Sodium bicarbonate administration during in-hospital pediatric cardiac arrest: A systematic review and meta-analysis.

BACKGROUND: Current American Heart Association Pediatric Life Support (PLS) guidelines do not recommend the routine use of sodium bicarbonate (SB) during cardiac arrest in pediatric patients. However, SB administration during pediatric resuscitation is still common in clinical practice. The objective of this study was to assess the impact of SB on mortality and neurological outcomes in pediatric patients with in-hospital cardiac arrest. METHODS: We searched PubMed, Embase, and the Cochrane Central Register of Controlled Trials from inception to January 2021. We included studies of pediatric patients that had two treatment arms (treated with SB or not treated with SB) during in-hospital cardiac arrest (IHCA). Risk of bias was assessed using the Newcastle-Ottawa Scale and the certainty of evidence was assessed using GRADE system. RESULTS: We included 7 observational studies with a total of 4877 pediatric in-hospital cardiac arrest patients. Meta-analysis showed that SB administration during pediatric cardiac resuscitation was associated with a significantly decreased rate of survival to hospital discharge (odds ratio [OR], 0.40; 95% confidence interval [CI], 0.25-0.63, p value = 0.0003). There were insufficient studies for 24-h survival and neurologic outcomes analysis. The subgroup analysis showed a significantly decreased rate of survival to hospital discharge in both the "before 2010" subgroup (OR 0.47; 95% CI 0.30-0.73; p value = 0.006) and the "after 2010" subgroup (OR 0.46; 95% CI 0.25-0.87; p value = 0.02). The certainty of evidence ranged from very low to low. CONCLUSIONS: This meta-analysis of non-randomized studies supported current PLS guideline that routine administration of SB is not recommended in pediatric cardiac arrest except in special resuscitation situations. TRIAL REGISTRATION: The protocol was registered with PROSPERO on 8 August 2020 (registration number: CRD42020197837).

Factors associated with outcomes in traumatic cardiac arrest patients without prehospital return of spontaneous circulation.

BACKGROUND: Prognostic factors for the outcomes in traumatic cardiac arrest (TCA) patients transported to hospitals without prehospital return of spontaneous circulation (ROSC) remain uncertain. The aim of this study is to investigate factors associated with outcomes in TCA patients without prehospital ROSC. METHODS: We conducted a retrospective cohort study using a multi-institutional, 5-year database. Only TCA patients without prehospital ROSC were included. The primary outcome was ROSC in the emergency department (ED), and the secondary outcome was 30-day survival. Logistic regression analysis was performed to determine the factors associated with primary and secondary outcomes. RESULTS: Among 463 TCA patients, 73 (16%) had ROSC during ED resuscitation, and among those with sustained ROSC, 10 (14%) survived for at least 30 days. Injury severity score ≧ 16 (OR, 0.06; 95% CI: 0.02-0.20), trauma center admission (OR, 2.69; 95% CI: 1.03-7.03), length of ED resuscitation (OR, 0.98; 95% CI: 0.96-0.99), and total resuscitation length > 20 min (OR, 0.21; 95% CI: 0.08-0.54) were associated with ROSC. CONCLUSIONS: In TCA patients transported to hospitals without prehospital ROSC, resuscitation attempts could be beneficial. We should aim to resuscitate patients as soon as possible with appropriate treatments for trauma patients, early activation of trauma team, and then, as a result, shorter resuscitation time will be achieved.

Macular edema might be a rare presentation of hydroxychloroquine-induced retinal toxicity.

The aim of this study is to report a rare case of macular edema as a presentation of hydroxychloroquine-related retinal toxicity. We presented a case of a 46-year-old female patient using hydroxychloroquine for underlying rheumatoid arthritis (RA) with blurred vision over the left eye. Uveitis and macular edema were found initially. Systemic survey did not reveal any other etiology. Topical corticosteroid was given under the impression of RA-related uveitis. The uveitis resolved 1 week later, but macular edema persisted in spite of treatment. Under the suspicion of drug-related complication, we try to discontinue hydroxychloroquine. Her symptoms improved gradually after cessation of hydroxychloroquine, and further serial image study confirmed subsiding of the macular edema without any further treatment. Except the well-known signs of the retinal toxicity, macular edema might be a rare presentation of hydroxychloroquine-related retinal toxicity.

Surgical results for consecutive exotropia.

PURPOSE: To evaluate the surgical results of medial rectus (MR) muscle advancement with or without recession of the antagonist muscle for consecutive exotropia. METHODS: Medical records of patients with consecutive exotropia (n = 27) were retrospectively reviewed. All patients received one-eye surgery with MR advancement, lateral rectus (LR) recession, or combined surgery. The pre- and post-operative angle of deviation was recorded. Characteristics were compared between groups. The follow-up period was at least 3 months. RESULTS: The overall successful rate was 62.96%, with 50% in MR advancement group, 60% in LR recession group, and 71.4% in combined group. Patients in combined group had larger preoperative deviation. There were comparable surgical results between patients with inferior oblique (IO) muscle overaction receiving correction simultaneously and patients without IO muscle overaction. CONCLUSIONS: The overall surgical successful rate for consecutive exotropia in this study was 62.96%. Combined MR advancement and LR recession yielded better results than MR advancement or LR recession alone although it was not statistically significant.

Divergent Alanyl-tRNA Synthetase Genes of Vanderwaltozyma polyspora Descended from a Common Ancestor through Whole-Genome Duplication Followed by Asymmetric Evolution.

Cytoplasmic and mitochondrial forms of a eukaryotic aminoacyl-tRNA synthetase (aaRS) are generally encoded by two distinct nuclear genes, one of eukaryotic origin and the other of mitochondrial origin. However, in most known yeasts, only the mitochondrial-origin alanyl-tRNA synthetase (AlaRS) gene is retained and plays a dual-functional role. Here, we present a novel scenario of AlaRS evolution in the yeast Vanderwaltozyma polyspora. V. polyspora possesses two significantly diverged AlaRS gene homologues, one encoding the cytoplasmic form and the other its mitochondrial counterpart. Clever selection of transcription and translation initiation sites enables the two isoforms to be localized and thus functional in their respective cellular compartments. However, the two isoforms can also be stably expressed and function in the reciprocal compartments by insertion or removal of a mitochondrial targeting signal. Synteny and phylogeny analyses revealed that the AlaRS homologues of V. polyspora arose from a dual-functional common ancestor through whole-genome duplication (WGD). Moreover, the mitochondrial form had higher synonymous (1.6-fold) and nonsynonymous (2.8-fold) substitution rates than did its cytoplasmic counterpart, presumably due to a lesser constraint imposed on components of the mitochondrial translational apparatus. Our study suggests that asymmetric evolution confers the divergence between the AlaRS paralogues of V. polyspora.

Functional substitution of a eukaryotic glycyl-tRNA synthetase with an evolutionarily unrelated bacterial cognate enzyme.

Two oligomeric types of glycyl-tRNA synthetase (GlyRS) are found in nature: a α2 type and a α2ß2 type. The former has been identified in all three kingdoms of life and often pairs with tRNAGly that carries an A73 discriminator base, while the latter is found only in bacteria and chloroplasts and is almost always coupled with tRNAGly that contains U73. In the yeast Saccharomyces cerevisiae, a single GlyRS gene, GRS1, provides both the cytoplasmic and mitochondrial functions, and tRNAGly isoacceptors in both compartments possess A73. We showed herein that Homo sapiens and Arabidopsis thaliana cytoplasmic GlyRSs (both α2-type enzymes) can rescue both the cytoplasmic and mitochondrial defects of a yeast grs1- strain, while Escherichia coli GlyRS (a α2ß2-type enzyme) and A. thaliana organellar GlyRS (a (αß)2-type enzyme) failed to rescue either defect of the yeast mull allele. However, a head-to-tail αß fusion of E. coli GlyRS effectively supported the mitochondrial function. Our study suggests that a α2-type eukaryotic GlyRS may be functionally substituted with a α2ß2-type bacterial cognate enzyme despite their remote evolutionary relationships.