Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale.

MOTIVATION: Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach which is highly accurate at only a small fraction of the cost. RESULTS: We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and Caenorhabditis elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ∼5%. AVAILABILITY AND IMPLEMENTATION: Analysis pipeline for this approach is available at GitHub as R package controlFreq (github.com/gimelbrantlab/controlFreq).

Efficacy of 10%,25% and 50% dextrose in the treatment of hypoglycemia in the emergency department - A randomized controlled study.

INTRODUCTION: Documented symptomatic hypoglycemia is defined as "event during which typical symptoms of hypoglycemia are accompanied by measured blood glucose of ≤70 mg/dL. Most of the studies and recommendations for the unconscious hypoglycemic adult advocate the use of 25 g of glucose as 50 mL of 50% dextrose solution intravenous or 1 mg of intramuscular glucagon. OBJECTIVE: To compare the efficacy and safety of 5 g boluses of 10%, 25% and 50% dextrose in the treatment of hypoglycemic patients presenting to our emergency department. METHODS: This was a randomized controlled single blinded study. Hypoglycemic patients in altered mental status were randomized into three treatment arms to be administered 10%, 25% or 50% dextrose. 5 g aliquots of intravenous 10%,25% or 50% dextrose were administered over 1 min. Time taken to achieve a Glasgow Coma Scale (GCS) of 15 and median total doses (g) were the primary outcomes. RESULTS: Data of 204 patients were analysed in the study. There was no difference in the median time to achieve a GCS of 15 in all three treatment arms (6 min). Total median dose administered in the 10% and 25% groups was lower than 50% (10 g vs 15 g). Proportion of patients who received the maximum dose of 25 g was higher in the 50% group as compared to 10% and 25% groups (12%, 3%, 4%). CONCLUSION: There was no difference in 10% dextrose and 25% dextrose as compared to 50% dextrose in achieving the baseline mental status (or GCS 15) in the treatment of hypoglycemia in the ED.

Female preferences for the spectral content of advertisement calls in Cope's gray treefrog (Hyla chrysoscelis).

Amphibians have inner ears with two sensory papillae tuned to different frequency ranges of airborne sounds. In frogs, male advertisement calls possess distinct spectral components that match the tuning of one or both sensory papillae. Female preferences for the spectral content of advertisement calls can depend on signal amplitude and can vary among closely related lineages. In this study of Cope's gray tree frog (Hyla chrysoscelis), we investigated the amplitude dependence of female preferences for the spectral content of male advertisement calls, which have a "bimodal" spectrum with separate low-frequency (1.25 kHz) and high-frequency (2.5 kHz) components. In two-alternative choice tests, females generally preferred synthetic calls with bimodal spectra over "unimodal" calls having only one of the two spectral components. They also preferred unimodal calls with a high-frequency component over one with the low-frequency component. With few exceptions, preferences were largely independent of amplitude across both a 30 dB range of overall signal amplitude and an 11 dB range in the relative amplitudes of the two spectral components. We discuss these results in the context of evolutionary lability in female preferences for the spectral content of advertisement calls in North American tree frogs in the genus Hyla.

Neural basis of acoustic species recognition in a cryptic species complex.

Sexual traits that promote species recognition are important drivers of reproductive isolation, especially among closely related species. Identifying neural processes that shape species differences in recognition is crucial for understanding the causal mechanisms of reproductive isolation. Temporal patterns are salient features of sexual signals that are widely used in species recognition by several taxa, including anurans. Recent advances in our understanding of temporal processing by the anuran auditory system provide an opportunity to investigate the neural basis of species-specific recognition. The anuran inferior colliculus consists of neurons that are selective for temporal features of calls. Of potential relevance are auditory neurons known as interval-counting neurons (ICNs) that are often selective for the pulse rate of conspecific advertisement calls. Here, we tested the hypothesis that ICNs mediate acoustic species recognition by exploiting the known differences in temporal selectivity in two cryptic species of gray treefrog (Hyla chrysoscelis and Hyla versicolor). We examined the extent to which the threshold number of pulses required to elicit behavioral responses from females and neural responses from ICNs was similar within each species but potentially different between the two species. In support of our hypothesis, we found that a species difference in behavioral pulse number thresholds closely matched the species difference in neural pulse number thresholds. However, this relationship held only for ICNs that exhibited band-pass tuning for conspecific pulse rates. Together, these findings suggest that differences in temporal processing of a subset of ICNs provide a mechanistic explanation for reproductive isolation between two cryptic treefrog species.

Qualitative study of loneliness in a senior housing community: the importance of wisdom and other coping strategies.

OBJECTIVE: Older adults are at a high risk for loneliness, which impacts their health, well-being, and longevity. While related to social isolation, loneliness is a distinct, internally experienced, distressing feeling. The present qualitative study sought to identify characteristics of loneliness in older adults living independently within a senior housing community, which is typically designed to reduce social isolation. METHOD: Semi-structured qualitative interviews regarding the experience of loneliness, risk factors, and ways to combat it were conducted with 30 older adults, ages 65-92 years. The interviews were audiotaped, transcribed, and coded using a grounded theory analytic approach based on coding, consensus, co-occurrence, and comparison. RESULTS: Three main themes with multiple subthemes are described: (A) Risk and Protective factors for loneliness: age-associated losses, lack of social skills or abilities, and protective personality traits; (B) Experience of loneliness: Sadness and lack of meaning as well as Lack of motivation; and (C) Coping strategies to prevent or overcome loneliness: acceptance of aging, compassion, seeking companionship, and environment enables socialization. DISCUSSION: Despite living within a communal setting designed to reduce social isolation, many older adults described feeling lonely in stark negative terms, attributing it to aging-associated losses or lack of social skills and abilities. However, interviewees also reported positive personal qualities and actions to prevent or cope with loneliness, several of which mirrored specific components of wisdom. The results support the reported inverse relationship between loneliness and wisdom and suggest a potential role for wisdom-enhancing interventions to reduce and prevent loneliness in older populations.

Drop impact on thin powder layers: pattern formation by air entrapment.

Impact of drops on thin powder layers displaces the powder particles radially outward producing shallow craters with thick rims, for example, as observed on dust layers on the floor. Here, we report that the patterns formed on thin powder layers by drop impact are not limited to such crater-like ones. Instead, depending upon the layer properties, disc or disc-plus-ring shaped patterns are formed at the impact point. We show that air entrapment and micro-bubble formation during the drop impact result in the formation of such patterns. Based on high-speed imaging, scaling analyses, and measurements with various liquids and powder layers, we propose a mechanism for the formation of such patterns. The phenomenon that we report can open further investigations on drop impact on the granular matter.

Treefrogs exploit temporal coherence to form perceptual objects of communication signals.

For many animals, navigating their environment requires an ability to organize continuous streams of sensory input into discrete 'perceptual objects' that correspond to physical entities in visual and auditory scenes. The human visual and auditory systems follow several Gestalt laws of perceptual organization to bind constituent features into coherent perceptual objects. A largely unexplored question is whether nonhuman animals follow similar Gestalt laws in perceiving behaviourally relevant stimuli, such as communication signals. We used females of Cope's grey treefrog (Hyla chrysoscelis) to test the hypothesis that temporal coherence-a powerful Gestalt principle in human auditory scene analysis-promotes perceptual binding in forming auditory objects of species-typical vocalizations. According to the principle of temporal coherence, sound elements that start and stop at the same time or that modulate coherently over time are likely to become bound together into the same auditory object. We found that the natural temporal coherence between two spectral components of advertisement calls promotes their perceptual binding into auditory objects of advertisement calls. Our findings confirm the broad ecological validity of temporal coherence as a Gestalt law of auditory perceptual organization guiding the formation of biologically relevant perceptual objects in animal behaviour.

Temporal expression profiling identifies pathways mediating effect of causal variant on phenotype.

Even with identification of multiple causal genetic variants for common human diseases, understanding the molecular processes mediating the causal variants' effect on the disease remains a challenge. This understanding is crucial for the development of therapeutic strategies to prevent and treat disease. While static profiling of gene expression is primarily used to get insights into the biological bases of diseases, it makes differentiating the causative from the correlative effects difficult, as the dynamics of the underlying biological processes are not monitored. Using yeast as a model, we studied genome-wide gene expression dynamics in the presence of a causal variant as the sole genetic determinant, and performed allele-specific functional validation to delineate the causal effects of the genetic variant on the phenotype. Here, we characterized the precise genetic effects of a functional MKT1 allelic variant in sporulation efficiency variation. A mathematical model describing meiotic landmark events and conditional activation of MKT1 expression during sporulation specified an early meiotic role of this variant. By analyzing the early meiotic genome-wide transcriptional response, we demonstrate an MKT1-dependent role of novel modulators, namely, RTG1/3, regulators of mitochondrial retrograde signaling, and DAL82, regulator of nitrogen starvation, in additively effecting sporulation efficiency. In the presence of functional MKT1 allele, better respiration during early sporulation was observed, which was dependent on the mitochondrial retrograde regulator, RTG3. Furthermore, our approach showed that MKT1 contributes to sporulation independent of Puf3, an RNA-binding protein that steady-state transcription profiling studies have suggested to mediate MKT1-pleiotropic effects during mitotic growth. These results uncover interesting regulatory links between meiosis and mitochondrial retrograde signaling. In this study, we highlight the advantage of analyzing allele-specific transcriptional dynamics of mediating genes. Applications in higher eukaryotes can be valuable for inferring causal molecular pathways underlying complex dynamic processes, such as development, physiology and disease progression.

arrayMap 2014: an updated cancer genome resource.

Somatic copy number aberrations (CNA) represent a mutation type encountered in the majority of cancer genomes. Here, we present the 2014 edition of arrayMap (http://www.arraymap.org), a publicly accessible collection of pre-processed oncogenomic array data sets and CNA profiles, representing a vast range of human malignancies. Since the initial release, we have enhanced this resource both in content and especially with regard to data mining support. The 2014 release of arrayMap contains more than 64,000 genomic array data sets, representing about 250 tumor diagnoses. Data sets included in arrayMap have been assembled from public repositories as well as additional resources, and integrated by applying custom processing pipelines. Online tools have been upgraded for a more flexible array data visualization, including options for processing user provided, non-public data sets. Data integration has been improved by mapping to multiple editions of the human reference genome, with the majority of the data now being available for the UCSC hg18 as well as GRCh37 versions. The large amount of tumor CNA data in arrayMap can be freely downloaded by users to promote data mining projects, and to explore special events such as chromothripsis-like genome patterns.

Structural basis for nuclear import of splicing factors by human Transportin 3.

Transportin 3 (Tnpo3, Transportin-SR2) is implicated in nuclear import of splicing factors and HIV-1 replication. Herein, we show that the majority of cellular Tnpo3 binding partners contain arginine-serine (RS) repeat domains and present crystal structures of human Tnpo3 in its free as well as GTPase Ran- and alternative splicing factor/splicing factor 2 (ASF/SF2)-bound forms. The flexible ß-karyopherin fold of Tnpo3 embraces the RNA recognition motif and RS domains of the cargo. A constellation of charged residues on and around the arginine-rich helix of Tnpo3 HEAT repeat 15 engage the phosphorylated RS domain and are critical for the recognition and nuclear import of ASF/SF2. Mutations in the same region of Tnpo3 impair its interaction with the cleavage and polyadenylation specificity factor 6 (CPSF6) and its ability to support HIV-1 replication. Steric incompatibility of the RS domain and RanGTP engagement by Tnpo3 provides the mechanism for cargo release in the nucleus. Our results elucidate the structural bases for nuclear import of splicing factors and the Tnpo3-CPSF6 nexus in HIV-1 biology.

Retroviral intasome assembly and inhibition of DNA strand transfer.

Integrase is an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The structure of full-length retroviral integrase, either separately or in complex with DNA, has been lacking. Furthermore, although clinically useful inhibitors of HIV integrase have been developed, their mechanism of action remains speculative. Here we present a crystal structure of full-length integrase from the prototype foamy virus in complex with its cognate DNA. The structure shows the organization of the retroviral intasome comprising an integrase tetramer tightly associated with a pair of viral DNA ends. All three canonical integrase structural domains are involved in extensive protein-DNA and protein-protein interactions. The binding of strand-transfer inhibitors displaces the reactive viral DNA end from the active site, disarming the viral nucleoprotein complex. Our findings define the structural basis of retroviral DNA integration, and will allow modelling of the HIV-1 intasome to aid in the development of antiretroviral drugs.

Progenetix: 12 years of oncogenomic data curation.

DNA copy number aberrations (CNAs) can be found in the majority of cancer genomes and are crucial for understanding the potential mechanisms underlying tumor initiation and progression. Since the first release in 2001, the Progenetix project (http://www.progenetix.org) has provided a reference resource dedicated to provide the most comprehensive collection of genome-wide CNA profiles. Reflecting the application of comparative genomic hybridization techniques to tens of thousands of cancer genomes, over the past 12 years our data curation efforts have resulted in a more than 60-fold increase in the number of cancer samples presented through Progenetix. In addition, new data exploration tools and visualization options have been added. In particular, the gene-specific CNA frequency analysis should facilitate the assignment of cancer genes to related cancer types. In addition, the new user file processing interface allows users to take advantage of the online tools, including various data representation options for proprietary data pre-publication. In this update article, we report recent improvements of the database in terms of content, user interface and online tools.

Juvenile Xanthogranuloma: Presenting as an Isolated Renal Involvement.

Juvenile xanthogranuloma (JXG) is a histiocytic disorder of childhood that mostly affects the skin although extracutaneous and visceral manifestations are well documented in English literature. The renal involvement is less commonly documented as a manifestation of xanthogranuloma and the reported cases occur in conjunction with cutaneous xanthogranuloma, especially in association with multiple skin lesions. We present a case of isolated renal JXG presenting as a renal mass with perinephric soft tissue and muscle involvement but without any cutaneous manifestation. This is the first case report of renal JXG without cutaneous involvement, to the best of our knowledge.

Quality characteristics of gluten free bread from barnyard millet-soy flour blends.

The effects of formulation of leavened bread by using varying levels (for 50 g base flour) of soy flour-barnyard millet blends (with 5.74, 6.25, 7, 7.75 and 8.26 g of soy flour), yeast (1.83, 2, 2.25, 2.5 and 2.67 g) and salt (0.63, 0.8, 1.05, 1.30 and 1.47 g) on textural, colour and specific volume were determined. A central composite rotatable design of response surface methodology was used to plan the experiments. The second order models obtained were observed to be statistically significant and capable of demonstrating the effects input variables on responses. All the textural properties were affected significantly by amount of soy flour and yeast in the dough. Soy flour had a significant effect on the colour of the bread making it more brown. Interaction of soy flour and yeast affected the specific volume to maximum extent. Two-tailed t test established that the efficacy of the models as no significant was observed between the predicted and the actual values.

Bromo- and extraterminal domain chromatin regulators serve as cofactors for murine leukemia virus integration.

Retroviral integrase (IN) proteins catalyze the permanent integration of proviral genomes into host DNA with the help of cellular cofactors. Lens epithelium-derived growth factor (LEDGF) is a cofactor for lentiviruses, including human immunodeficiency virus type 1 (HIV-1), and targets lentiviral integration toward active transcription units in the host genome. In contrast to lentiviruses, murine leukemia virus (MLV), a gammaretrovirus, tends to integrate near transcription start sites. Here, we show that the bromodomain and extraterminal domain (BET) proteins BRD2, BRD3, and BRD4 interact with gammaretroviral INs and stimulate the catalytic activity of MLV IN in vitro. We mapped the interaction site to a characteristic structural feature within the BET protein extraterminal (ET) domain and to three amino acids in MLV IN. The ET domains of different BET proteins stimulate MLV integration in vitro and, in the case of BRD2, also in vivo. Furthermore, two small-molecule BET inhibitors, JQ1 and I-BET, decrease MLV integration and shift it away from transcription start sites. Our data suggest that BET proteins might act as chromatin-bound acceptors for the MLV preintegration complex. These results could pave a way to redirecting MLV DNA integration as a basis for creating safer retroviral vectors.

Examining structural analogs of elvitegravir as potential inhibitors of HIV-1 integrase.

Acquired immunodeficiency syndrome (AIDS) is a major health problem in many parts of the world. The human immunodeficiency virus-1 integrase (HIV-1 IN) enzyme has been targeted in HIV patients for therapy. Several integrase inhibitors have been reported, but only elvitegravir (EVG), a new-generation drug, is clinically approved for HIV treatment. In the present work, we investigated two structural analogs of EVG as potential inhibitors of the target molecule, HIV-1 IN. The ligand binding site on HIV-1 IN was identified using Q-SiteFinder, and the HIV-1 IN protein was docked with ligand (EVG and/or analogs) using AutoDock 4. The results suggest that Lys173, Thr125, and His171 are involved in enzyme-substrate binding through hydrogen bonds. Single mutations carried out at Lys173, viz. Lys173Leu (polar > nonpolar) and Lys173Gln (polar > polar), in chain B using PyMOL showed the mutants to have lower binding energy when docked with analog 2, suggesting it to be more stable than analog 1. In conclusion, the mutant HIV-1 IN can bind EVG and its analogs. The physicochemical and pharmacokinetic parameters also show analog 2 to be a promising molecule that can be developed as an alternative to EVG to help overcome the problem of drug resistance by HIV to this inhibitor. Analog 2 may be used as an HIV-1 IN inhibitor with similar potential to that of EVG. Further validation through wet-lab studies, however, is required for future applications.

Bridging the Mind and Gut: Uncovering the Intricacies of Neurotransmitters, Neuropeptides, and their Influence on Neuropsychiatric Disorders.

BACKGROUND: The gut-brain axis (GBA) is a bidirectional signaling channel that facilitates communication between the gastrointestinal tract and the brain. Recent research on the gut-brain axis demonstrates that this connection enables the brain to influence gut function, which in turn influences the brain and its cognitive functioning. It is well established that malfunctioning of this axis adversely affects both systems' ability to operate effectively. OBJECTIVE: Dysfunctions in the GBA have been associated with disorders of gut motility and permeability, intestinal inflammation, indigestion, constipation, diarrhea, IBS, and IBD, as well as neuropsychiatric and neurodegenerative disorders like depression, anxiety, schizophrenia, autism, Alzheimer's, and Parkinson's disease. Multiple research initiatives have shown that the gut microbiota, in particular, plays a crucial role in the GBA by participating in the regulation of a number of key neurochemicals that are known to have significant effects on the mental and physical well-being of an individual. METHODS: Several studies have investigated the relationship between neuropsychiatric disorders and imbalances or disturbances in the metabolism of neurochemicals, often leading to concomitant gastrointestinal issues and modifications in gut flora composition. The interaction between neurological diseases and gut microbiota has been a focal point within this research. The novel therapeutic interventions in neuropsychiatric conditions involving interventions such as probiotics, prebiotics, and dietary modifications are outlined in this review. RESULTS: The findings of multiple studies carried out on mice show that modulating and monitoring gut microbiota can help treat symptoms of such diseases, which raises the possibility of the use of probiotics, prebiotics, and even dietary changes as part of a new treatment strategy for neuropsychiatric disorders and their symptoms. CONCLUSION: The bidirectional communication between the gut and the brain through the gut-brain axis has revealed profound implications for both gastrointestinal and neurological health. Malfunctions in this axis have been connected to a range of disorders affecting gut function as well as cognitive and neuropsychiatric well-being. The emerging understanding of the role of gut microbiota in regulating key neurochemicals opens up possibilities for novel treatment approaches for conditions like depression, anxiety, and neurodegenerative diseases.

Managing Patients With Sympathetic Crashing Acute Pulmonary Edema (SCAPE) Using the SCAPE Treatment Protocol: A Case Series.

Pulmonary edema refers to the accumulation of excessive fluid in the alveolar walls and alveolar spaces of the lungs. It is a life-threatening condition with a high mortality rate and requires immediate assessment and management. Use of intravenous nitroglycerin has been advocated for such cases. The authors present a case series of 3 patients who presented to the emergency department with sympathetic crashing acute pulmonary edema (SCAPE) and were managed with high-dose intravenous nitroglycerin and bilevel positive airway pressure support using the SCAPE treatment protocol, leading to early correction of blood pressure, avoidance of endotracheal intubation, and no episodes of hypotension or rebound hypertension. The authors recommend emergency physicians utilize the SCAPE treatment protocol while managing patients with SCAPE.

ChatGPT 3.5 fails to write appropriate multiple choice practice exam questions.

Artificial intelligence (AI) may have a profound impact on traditional teaching in academic settings. Multiple concerns have been raised, especially related to using ChatGPT for creating de novo essays. However, AI programs such as ChatGPT may augment teaching techniques. In this article, we used ChatGPT 3.5 to create 60 multiple choice questions. Author written text was uploaded and ChatGPT asked to create multiple choice questions with an explanation for the correct answer and explanations for the incorrect answers. Unfortunately, ChatGPT only generated correct questions and answers with explanations in 32 % of the questions (19 out of 60). In many instances, ChatGPT failed to provide an explanation for the incorrect answers. An additional 25 % of the questions had answers that were either wrong or misleading. A grade of 32 % would be considered failing in most courses. Despite these issues, instructors may still find ChatGPT useful for creating practice exams with explanations-with the caveat that extensive editing may be required.