Miracle-dz/UniFAR-FTUs huggingface dataset:
Scar formation in mice deafened with kanamycin and furosemide

In mammals, hair cell loss is irreversible and leads to hearing loss. To develop and test the functioning of different strategies aiming at hair cell regeneration, animal models of sensorineural hearing loss are essential. Although cochleae of these animals should lack hair cells, supporting cells should be preserved forming an environment for the regenerated hair cells. In this study, we investigated how ototoxic treatment with kanamycin and furosemide changes the structure of cochlear sensory epithelium in mice. The study also compared different tissue preparation protocols for scanning electron microscopy (SEM). Cochleae were collected from deafened and nondeafened mice and further processed for plastic mid modiolar sections and SEM. For comparing SEM protocols, cochleae from nondeafened mice were processed using three protocols: osmium–thiocarbohydrazide–osmium (OTO), tannic acid–arginine–osmium, and the conventional method with gold‐coating. The OTO method demonstrated optimal cochlear tissue preservation. Histological investigation of cochleae of deafened mice revealed that the supporting cells enlarged and ultimately replaced the lost hair cells forming types 1 and 2 phalangeal scars in a base towards apex gradient. The type 3 epithelial scar, flattened epithelium, has not been seen in analysed cochleae. The study concluded that mice deafened with kanamycin and furosemide formed scars containing supporting cells, which renders this mouse model suitable for testing various hair cell regeneration approaches. Microsc. Res. Tech. 79:766–772, 2016. © 2016 Wiley Periodicals, Inc.
Drainage Patterns to Nontraditional Nodal Regions and Level IIB in Cutaneous Head and Neck Malignancy

Objectives (1) Determine the frequency of nontraditional sentinel lymph node (SLN) locations in cutaneous head and neck malignancy and (2) determine the frequency of level IIB SLNs in cutaneous head and neck malignancy. Design Case series with chart review. Setting Tertiary academic hospital. Subjects and Methods In total, 145 consecutive sentinel lymph node biopsy (SLNB) specimens for cutaneous head and neck malignancies were reviewed from 2007 to 2015. Nodal regions were categorized into levels I to V, parotid, external jugular (EJ), perifacial, suboccipital, and postauricular regions. Primary locations were divided into scalp, forehead, cheek, ear, neck, nose, periocular, and lip. Frequencies of sentinel lymph node (SLN) locations for each primary location were determined. Results Parotid, EJ, perifacial, suboccipital, postauricular, and level IIB lymph SLNs were identified as nontraditional lymph node regions at risk in head and neck cutaneous malignancy. EJ SLNs were present in over 15% of all cases and over 25% of periocular and cheek lesions. Perifacial SLNs were frequently present in nose and lip lesions. Suboccipital and postauricular nodes were only present in scalp lesions. Level II was the most common location for a SLN. In total, 15.9% of all cases involved level IIB. Scalp and ear primary lesions were most likely to drain to level IIB. Conclusions Nontraditional SLN locations, such as EJ, perifacial, suboccipital, postauricular, and parotid, as well as level IIB, are important sites of drainage for head and neck cutaneous malignancy. Prediction of at-risk lymph node regions is important to help guide SLNBs, elective and completion neck lymphadenectomy and radiation, and long-term observation.
In vitro characterization of cell‐level neurophysiological diversity in the rostral nucleus reuniens of adult mice

The nucleus reuniens (Re), a nucleus of the midline thalamus, is part of a cognitive network including the hippocampus and the medial prefrontal cortex. To date, very few studies have examined the electrophysiological properties of Re neurons at a cellular level. The majority of Re neurons exhibit spontaneous action potential firing at rest. This is independent of classical amino‐acid mediated synaptic transmission. When driven by various forms of depolarizing current stimulus, Re neurons display considerable diversity in their firing patterns. As a result of the presence of a low threshold Ca2+ channel, spike output functions are strongly modulated by the prestimulus membrane potential. Finally, we describe a novel form of activity‐dependant intrinsic plasticity that eliminates the high‐frequency burst firing present in many Re neurons. These results provide a comprehensive summary of the intrinsic electrophysiological properties of Re neurons allowing us to better consider the role of the Re in cognitive processes.
Multiple Socioeconomic Factors and Dental Caries in Swedish Children and Adolescents

The study aimed to explore associations between multiple socioeconomic factors and dental caries experience in Swedish children and adolescents (3-19 years old). Electronic dental records from 300,988, in a Swedish region (97.3% coverage) were collected using the DMFT indices (decayed, missing, filled teeth: dependent variables). Socioeconomic status (SES) data (ethnicity, wealth, parental education, and employment) for individuals, parents, and families were obtained from official registers. Principal component analysis was used to explore SES data. Scores based on the first factor were used as an independent aggregated socioeconomic variable in logistic regression analyses. Dental caries experience was low in the participants: 16% in 3- to 6-year-olds (deft index: decayed, extracted, filled teeth) and 47% in 7- to 19-year-olds (DFT index). Both separate and aggregated socioeconomic variables were consistently associated with the dental caries experience irrespective of the caries index used: the crude odds ratio (OR) for having at least 1 caries lesion in 3- to 6-year-olds (deft index) in the lowest SES quintile was 3.26 (95% confidence interval [CI] 3.09-3.43) and in ≥7-year-olds (DFT index) OR 1.80 (95% CI 1.75-1.84) compared with children in the 4 higher SES quintiles. Overall, associations were stronger in the primary dentition than in the permanent dentition. Large SES models contributed more to explaining the caries experience than slim models including fewer SES indicators. In conclusion, socioeconomic factors were consistently associated with dental caries experience in the children and adolescents both as single factors and as multiple factors combined in an index. Socioeconomic inequalities had stronger associations to caries experience in young children than in older children and adolescents.
“Homework Feedback Is…”: Elementary and Middle School Teachers’ Conceptions of Homework Feedback

This study explored mathematics teachers’ conceptions of the homework feedback focusing on four key aspects: definition, purpose, types, and perceived impact. Forty-seven teachers from elementary and middle schools participated in six focus groups. Data were analyzed using content analysis. To enhance the trustworthiness of findings, classroom observations were used for triangulation of data. Participants conceptualized homework feedback in three directions (i.e., teachers’ feedback provided to students, students’ feedback provided to teachers, and homework self-feedback), being teachers’ monitoring of students’ learning the purpose reported by most teachers. Participants also reported the types of homework feedback more frequently used in class (e.g., checking homework completion, checking homework on the board), and their perceived impact on students. Findings provide valuable information to deepen the understanding of the homework feedback process, which may help develop new avenues for future research.
A general statistical framework for subgroup identification and comparative treatment scoring

Many statistical methods have recently been developed for identifying subgroups of patients who may benefit from different available treatments. Compared with the traditional outcome‐modeling approaches, these methods focus on modeling interactions between the treatments and covariates while by‐pass or minimize modeling the main effects of covariates because the subgroup identification only depends on the sign of the interaction. However, these methods are scattered and often narrow in scope. In this article, we propose a general framework, by weighting and A‐learning, for subgroup identification in both randomized clinical trials and observational studies. Our framework involves minimum modeling for the relationship between the outcome and covariates pertinent to the subgroup identification. Under the proposed framework, we may also estimate the magnitude of the interaction, which leads to the construction of scoring system measuring the individualized treatment effect. The proposed methods are quite flexible and include many recently proposed estimators as special cases. As a result, some estimators originally proposed for randomized clinical trials can be extended to observational studies, and procedures based on the weighting method can be converted to an A‐learning method and vice versa. Our approaches also allow straightforward incorporation of regularization methods for high‐dimensional data, as well as possible efficiency augmentation and generalization to multiple treatments. We examine the empirical performance of several procedures belonging to the proposed framework through extensive numerical studies.
Expression of Neuropeptide F Gene and Its Regulation of Feeding Behavior in the Pea Aphid, Acyrthosiphon pisum

Neuropeptide F (NPF) signaling systems are widespread and highly evolutionarily conserved from vertebrates to invertebrates. In fact, NPF has been identified in many insect species and plays regulatory roles in diverse physiological processes, such as feeding, learning, reproduction and stress responses. NPF operates by interacting with the NPF receptor (NPFR). Here, we characterized and determined the presumed role of NPF signaling in the wingless parthenogenetic pea aphid, Acyrthosiphon pisum. Quantitative real-time reverse transcription-PCR (qRT-PCR) revealed that the expression levels of both NPF and NPFR transcripts varied across developmental stages, which implies that the NPF signaling system might participate in the developmental regulation of aphid physiological processes or behaviors. The NPF transcript was mainly detected in the head but not in the gut, whereas the NPFR transcript was mainly detected in both the gut and head. In addition, the NPF transcript levels were markedly up-regulated in starved aphids compared with satiated aphids, and the transcript levels recovered after re-feeding. In contrast, the NPFR transcript levels remained stable in starved and re-fed aphids. Furthermore, RNAi knockdown by the injection of NPF dsRNA into wingless adult aphids significantly reduced their food intake. Further analysis of the modification of aphid feeding behavior on broad bean plants using electrical penetration graphs (EPGs) revealed that both the probing time and the total duration of phloem activity decreased significantly in the NPF treatment group. These results indicated a lower appetite for food after NPF knockdown, which could explain the reduction in aphid food intake. NPF silencing was also shown to reduce reproduction but not survival in aphids. Overall, the results of these experiments suggest that NPF plays an important role in regulation of feeding in A. pisum.
Dual pH with Multichannel Intraluminal Impedance Testing in the Evaluation of Subjective Laryngopharyngeal Reflux Symptoms

Objectives Minimal data exist to define the use of contemporary dual pH with multichannel intraluminal impedance (MII) probes integrating both pharyngeal acid and impedance sensors to evaluate laryngopharyngeal reflux (LPR) symptoms in a laryngology clinic population. This study was performed to review a series of patients tested with dual pH-MII for suspected LPR symptoms and to analyze pH-MII data findings for this patient cohort. Study Design Case series with planned data collection. Setting Tertiary laryngology clinic. Subjects and Methods Patients with symptoms suggestive of possible LPR (dysphonia, chronic cough, globus sensation, subglottic stenosis,) were evaluated with a dual pH-MII system, as well as previously validated reflux finding score (RFS) and reflux symptom index (RSI) instruments. Results A total of 109 patients were evaluated with dual pH-MII studies between 2010 and 2015, with 51 (47%) studies interpreted as “positive” for evidence of significant LPR, 43 (39%) as “negative,” and 15 (14%) as “equivocal. ” Dual pH-MII data analysis showed that positive studies had an average of 2.84 pharyngeal acid exposures below pH 4 (vs 0.28 for negative) and 46 episodes of proximal reflux exposure (either acid or nonacid) by impedance detection (vs 30.6 for negative). RSI scores were significantly different between positive and negative studies, while RFS scores were not. Conclusions Dual pH-MII analysis is a useful supplementary tool to provide objective evidence of pharyngeal reflux exposure in patients with suspected LPR. RSI scores appear to correlate with objective evidence of acid exposure in the pharynx, while RFS scores do not.
Children With Retinopathy-negative Cerebral Malaria: A Pathophysiologic Puzzle

Background: Cerebral malaria, defined as otherwise unexplained coma in a patient with circulating parasitemia, is a common disease in the developing world. The clinical diagnosis lacks specificity and children with other underlying causes of coma might be misdiagnosed as having cerebral malaria. The presence of malarial retinopathy can be used to differentiate children whose comas are caused by Plasmodium falciparum and its attendant pathophysiologies from those with other reasons for their abnormal mental status. Children with cerebral malaria who lack malarial retinopathy have not previously been described. Methods: All patients admitted to Queen Elizabeth Central Hospital in Blantyre, Malawi, during a 12-month period with a clinical diagnosis of cerebral malaria were evaluated for the presence of malarial retinopathy. Thirty-two patients lacked retinopathy findings. Clinical, laboratory, and radiologic information data were collected. Results: Thirty-two cases of retinopathy-negative cerebral malaria are presented. Conclusions: Children with retinopathy-negative cerebral malaria share a common clinical phenotype with lower rates of mortality compared with those who have malarial retinopathy. There are at least 4 possible pathophysiologic explanations for this common condition.
' s personal copy Cloud water composition over the southeastern Paci fi c Ocean during the VOCALS regional experiment

Relatively few measurements exist of cloud water composition over the open ocean, despite the importance of clouds as processors of atmospheric aerosols and trace gases in such regions. In order to improve understanding of cloud water composition in the southeast Pacific, and to determine the capacity of regional clouds for aqueous sulfate production, cloud water was collected aboard the NCAR C-130 during VOCALS-REx (VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment) in October and November, 2008. A total of 72 cloud water samples were collected on 14 flights using the NCAR/CSU airborne cloud water collector. Cloud water samples were collected over a region extending from approximately 71e85 west and from approximately 18e30 south. Cloud water pH ranged from 2.9 to 7.2 with an average of 4.3. Samples were also analyzed for major inorganic ions, hydrogen peroxide, sulfur(IV), carboxylic and dicarboxylic acids, formaldehyde, total Fe and Mn, and total organic carbon. Sodium and chloride were the most abundant solutes, while organic matter was found to contribute only 12%, on average, of the total measured solute load. Cloud water and trace gas measurements aboard the aircraft were used to examine the importance of various oxidation pathways for in-cloud sulfate production. S(IV) oxidation by H2O2 was found to be the most important pathway and excess cloud water H2O2 concentrations revealed considerable potential for additional, rapid in-cloud sulfate production by this mechanism. S(IV) oxidation by ozone was important when cloud water pH climbed above 5.5 and was the fastest oxidation pathway 24% of the time. 2011 Elsevier Ltd. All rights reserved.
The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies

Abstract Many viroids and RNA viruses have genomes that exhibit secondary structure, with paired nucleotides forming stems and loops. Such structures violate a key assumption of most methods of phylogenetic reconstruction, that sequence change is independent among sites. However, phylogenetic analyses of these transmissible agents rarely use evolutionary models that account for RNA secondary structure. Here, we assess the effect of using RNA-specific nucleotide substitution models on the phylogenetic inference of viroids and RNA viruses. We obtained data sets comprising full-genome nucleotide sequences from six viroid and ten single-stranded RNA virus species. For each alignment, we inferred consensus RNA secondary structures, then evaluated different DNA and RNA substitution models. We used model selection to choose the best-fitting model and evaluate estimated Bayesian phylogenies. Further, for each data set we generated and compared Robinson–Foulds (RF) statistics in order to test whether the distributions of trees generated under alternative models are notably different to each other. In all alignments, the best-fitting model was one that considers RNA secondary structure: RNA models that allow a nonzero rate of double substitution (RNA16A and RNA16C) fitted best for both viral and viroid data sets. In 14 of 16 data sets, the use of an RNA-specific model led to significantly longer tree lengths, but only in three cases did it have a significant effect on RFs. In conclusion, using RNA model when undertaking phylogenetic inference of viroids and RNA viruses can provide a better model fit than standard approaches and model choice can significantly affect branch length estimates.
De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq

Background The yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited. Methodology and principal findings Illumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp. A total of 9093 unigenes showed significant similarities to known proteins in public databases: 4477 and 6391 of B. yarrelli unigenes were mapped to the Gene Ontology (GO) and Clusters of Orthologous Groups (COG) databases, respectively. Moreover, 9635 unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, 8568 microsatellites (simple sequence repeats, SSRs) were detected, and 31 pairs of polymorphic primers were characterized using wild populations of B. yarrelli from the Nujiang River, Yunnan Province, China. Conclusion/Significance These sequences enrich the genomic resources for B. yarrelli and will benefit future investigations into the evolutionary and biological processes of this and related Bagarius species. The SSR markers developed in this study will facilitate construction of genetic maps, investigations of genetic structures and germplasm polymorphism assessments in B. yarrelli.
The dead and the dying - a difficult part of EMS transport: A Swiss cross-sectional study

Objective Most deaths occur in the pre-hospital setting, whereas mortality in the emergency department (ED) is low (<1%). However, our clinical impression is that some patients are being transported to hospital in devastating conditions with no likelihood of survival, but demanding extensive hospital resources. The decision on whether to transport a dying person to hospital or not is a difficult task for emergency medical services (EMS) personnel. As there is little epidemiological data about these patients, this paper aims to describe this special population. Methods Retrospective cross-sectional study on adult patients transported by ground ambulance to the ED of a Swiss university hospital, who died during their stay in the ED between January 2008 and December 2012. Data was collected on the basis of ambulance report forms and discharge summaries of the ED. Results One hundred and sixty-one patients were analysed. Most deaths were due to cardiovascular diseases (43%). Only 9% of patients died of trauma. The median age was 70 years (IQR 56–81 years) and 70% (n = 112) were men. Trauma patients were significantly younger (median age 55 years, p<0.001). The overall mortality rate was 0.9% for all patients transported by EMS to the ED. About one third of all patients received cardiopulmonary resuscitation (CPR) from bystanders (n = 53). The most common electrocardiogram (ECG) findings were asystole (n = 57) and pulseless electrical activity (n = 91). Fifty percent (n = 64) of the resuscitated patients were defibrillated. Three quarters (n = 115, 72%) of all patients were intubated on site. The mechanical chest compression device Lucas™2 was mainly used in cases of cardiovascular or uncertain cause of death and did not reduce the operating time on site. Conclusion The low ED mortality rate of 0.9% shows that only a few dying patients are transported to hospital. However, transport to hospital has to be carefully evaluated, especially for elderly patients with asystole or PEA due to medical conditions. The low CPR rate from bystanders demonstrates that public CPR training should be promoted further. The use of Lucas™2 did not reduce the operating time on site. For further investigations, comparison with survivors would be needed.
Regional grassland productivity responses to precipitation during multiyear above‐ and below‐average rainfall periods

There is considerable uncertainty in the magnitude and direction of changes in precipitation associated with climate change, and ecosystem responses are also uncertain. Multiyear periods of above‐ and below‐average rainfall may foretell consequences of changes in rainfall regime. We compiled long‐term aboveground net primary productivity (ANPP) and precipitation (PPT) data for eight North American grasslands, and quantified relationships between ANPP and PPT at each site, and in 1–3 year periods of above‐ and below‐average rainfall for mesic, semiarid cool, and semiarid warm grassland types. Our objective was to improve understanding of ANPP dynamics associated with changing climatic conditions by contrasting PPT–ANPP relationships in above‐ and below‐average PPT years to those that occurred during sequences of multiple above‐ and below‐average years. We found differences in PPT–ANPP relationships in above‐ and below‐average years compared to long‐term site averages, and variation in ANPP not explained by PPT totals that likely are attributed to legacy effects. The correlation between ANPP and current‐ and prior‐year conditions changed from year to year throughout multiyear periods, with some legacy effects declining, and new responses emerging. Thus, ANPP in a given year was influenced by sequences of conditions that varied across grassland types and climates. Most importantly, the influence of prior‐year ANPP often increased with the length of multiyear periods, whereas the influence of the amount of current‐year PPT declined. Although the mechanisms by which a directional change in the frequency of above‐ and below‐average years imposes a persistent change in grassland ANPP require further investigation, our results emphasize the importance of legacy effects on productivity for sequences of above‐ vs. below‐average years, and illustrate the utility of long‐term data to examine these patterns.