Miracle-dz/UniFAR-FTUs huggingface dataset:
A new cryptic frog species of the Mantidactylus boulengeri group with a divergent vocal sac structure

We describe a new frog species of the Mantidactylus boulengeri group (Amphibia: Anura: Mantellidae) in the subgenus Gephyromantis from south-eastern Madagascar. It is morphologically similar to M. eiselti and M. thelenae but differs in its advertisement calls with a distinctly shorter note duration, and in its bilobate (not single) subgular vocal sac. Like M. eiselti and M. thelenae the new species Mantidactylus enki is predominantly diurnal and calling males do not aggregate close to water bodies, indicating direct development as it has been demonstrated previously in M. eiselti. The advertisement calls of all three species are described in detail. A comparison with a further pair of cryptic species with bilobate vs. single subgular vocal sac (Mantidactylus tschenki — M. cornutus) did not reveal any consistent pattern of call variation correlated with vocal sac structure. Therefore, sexual selection may also be considered to explain differences in the colour and external structure of vocal sacs among closely related species.
Views and experiences of care home staff on managing behaviours that challenge in dementia: a national survey in England

ABSTRACT Aim: To determine the views of care home (CH) staff in relation to experiencing and managing behaviour that challenges (BtC) in dementia and their experiences of training. Method: Cross-sectional survey using a self-report questionnaire, distributed to staff employed in a 20% sample of all registered dementia-specialist CHs in England, either by postal or direct distribution. Results: Questionnaires were returned from 352 care staff (25%), representing 5% of all dementia-specialist CHs, half were CH without nursing. Respondents estimated caring for 14,585 residents, 9,361 with dementia and 5,258 with BtC. 30.2% of residents with dementia were estimated as being prescribed a medicine to control BtC. BtC reported as experienced by most respondents were: shouting (96.6%), verbal aggression (96.3%) and physical aggression (95.7%), with physical aggression viewed as most difficult to manage. Top behaviours experienced every shift were: wandering (77.8%), perseveration (68.2%) and restlessness (68.2%). Approaches such as assessing residents, knowing them and treating them as individuals, identifying triggers, having time for them and using an appropriate style of communication, were viewed as key to managing BtC, rather than guideline-specific interventions such as massage, aromatherapy and animal-assisted therapy. Only 38% agreed/strongly agreed medicines were useful to control BtC, which was related to the extent to which they were prescribed. Training was available, but variable in quality with on-line training being least useful and on-the job training most desirable. Conclusion: BtC are commonly and frequently experienced by care staff, who consider individual approaches, having time and good communication are key to successful management.
Age at menarche and risk of colorectal adenoma

Background/Aims Limited data are available regarding the association between age at menarche and the risk of colorectal adenoma. Therefore, we aimed to evaluate the relationship between reproductive factors including age at menarche and the risk of colorectal adenoma. Methods A cross-sectional study was performed on asymptomatic female subjects who underwent colonoscopy between 2010 and 2014 as part of a comprehensive health screening program in Korea. The association between reproductive factors including age at menarche and the presence of adenomas was assessed using multivariate logistic regression analysis. Results Among 32,620 asymptomatic female subjects, the proportion of patients with menarche at 10 to 11, 12 to 13, 14 to 15, 16 to 17, and 18 to 19 years of age was 4.1%, 31.7%, 45.4%, 14.9%, and 4.0%, respectively. Age at menarche was not significantly associated with the risk of any adenoma (adjusted odds ratio [AOR], 0.99; 95% confidence interval [CI], 0.97 to 1.02; p = 0.500) or advanced adenoma (AOR, 0.98; 95% CI, 0.91 to 1.04; p = 0.468) after adjusting for confounding factors. Age at menarche was not significantly associated with the risk of adenoma even among similar age groups. In addition, parity, use of female hormones, and menopause were not associated with the risk of adenoma. Conclusions Age at menarche, parity, use of female hormones, and menopause were not significantly associated with the risk of colorectal adenoma. Our findings indicate that reproductive factors including age at menarche do not affect the development of colorectal adenoma.
Investigations of Brain Network Alterations in Epilepsy Using Functional Magnetic Resonance Imaging

Epilepsy is a chronic condition characterized by recurrent unprovoked seizures with potentially disabling effects. These seizures, even when generated from a single focus, are believed to involve an extensive network of regions across the brain (Norden & Blumenfeld 2002). The propagation across these networks is responsible for the complex events associated with seizures including altered consciousness and motor phenomena. Additionally, repeated seizures can also produce chronic deficits that persist in between seizures, mainly cognitive deficits, primarily of memory and language related functions (Helmstaedter, et al. 2003). It is likely that these cognitive effects can be related to measurable brain network alterations as well. The non-invasive quantification of alterations in brain networks related to epilepsy is critical in determining the mechanisms of epileptogenesis and its treatments. In addition, it may also identify imaging biomarkers of epilepsy which can be used to diagnose and monitor these patients. Electroencephalography (EEG) is the most widely used method to quantify epileptic activity across the brain. The high temporal resolution of EEG measurements is advantageous in detecting the electrophysiological activity that defines the seizure focus and associated network. However, these techniques have relatively low spatial resolution when performed non-invasively, and can be corrupted by attenuation of the signal by bone or other tissue. Invasive EEG monitoring can measure electrical activity directly from the cortex, but the spatial resolution is still relatively low. The recording can only be obtained from preselected regions of the cortex. This method also involves more significant risk than non-invasive methods, but can be useful in detecting limited networks of epileptic activity (Blumenfeld, et al. 2004b, Englot, et al. 2008, Guye, et al. 2006). Imaging methodologies make it possible to investigate networks across the whole brain without the need for identifying predefined regions. Some non-invasive, low spatial resolution techniques to detect epileptic networks include interictal positron emission tomography (PET) with [18F] fluoro-2-deoxy-glucose (FDG) (Cascino & Jack 1996, Spencer & Bautista 2000) and ictal single-photon emission computed tomography (SPECT) imaging (Cascino & Jack 1996, Spencer & Bautista 2000). In general, these methods attempt to detect regions of metabolic (PET) or perfusion (SPECT) changes during the interictal state or ictal events. Studies have detected widespread brain networks associated with seizures using
K-RAS GENE CODON 12 MUTATION IN PANCREATIC TISSUE OF PATIENTS WITH PANCREATIC CANCER

The aim of this study was to analyze K-ras codon 12 mutation in the pancreatic tissue of Serbian patients with pancreatic cancer and assess whether the given mutation can be used as a molecular marker for this disease. The study was performed on pancreatic tissue samples obtained from 40 patients with clinical diagnosis of pancreatic cancer. The presence of K-ras codon 12 mutation was analyzed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Our study showed that K-ras mutation is present with a high frequency (66%) in the pancreatic tissue of patients with pancretic cancer.
Landscape of Microsatellite Instability Across 39 Cancer Types.

Purpose Microsatellite instability (MSI) is a pattern of hypermutation that occurs at genomic microsatellites and is caused by defects in the mismatch repair system. Mismatch repair deficiency that leads to MSI has been well described in several types of human cancer, most frequently in colorectal, endometrial, and gastric adenocarcinomas. MSI is known to be both predictive and prognostic, especially in colorectal cancer; however, current clinical guidelines only recommend MSI testing for colorectal and endometrial cancers. Therefore, less is known about the prevalence and extent of MSI among other types of cancer. Methods Using our recently published MSI-calling software, MANTIS, we analyzed whole-exome data from 11,139 tumor-normal pairs from The Cancer Genome Atlas and Therapeutically Applicable Research to Generate Effective Treatments projects and external data sources across 39 cancer types. Within a subset of these cancer types, we assessed mutation burden, mutational signatures, and somatic variants associated with MSI. Results We identified MSI in 3.8% of all cancers assessed-present in 27 of tumor types-most notably adrenocortical carcinoma (ACC), cervical cancer (CESC), and mesothelioma, in which MSI has not yet been well described. In addition, MSI-high ACC and CESC tumors were observed to have a higher average mutational burden than microsatellite-stable ACC and CESC tumors. Conclusion We provide evidence of as-yet-unappreciated MSI in several types of cancer. These findings support an expanded role for clinical MSI testing across multiple cancer types as patients with MSI-positive tumors are predicted to benefit from novel immunotherapies in clinical trials.
Adaptive divergence in the Superb Fairy-wren (Malurus cyaneus): a mainland versus island comparison of morphology and foraging behaviour

Abstract Understanding patterns of adaptive divergence is a cornerstone for understanding the process of speciation. The theory of ecological speciation predicts that natural selection shapes adaptive divergence. In this observational study, we examined the first phase of ecological speciation, namely adaptive divergence in foraging behaviour and morphology across populations (island and mainland sites) of the sexually dimorphic Superb Fairy- wren (Malurus cyaneus) that have been separated for approximately 9000 years. Current island theory predicts larger body-size in island species, as well as more generalist foraging and occupation of a wider ecological niche that is favoured by large body-size. We examined the vegetation structure across replicate study areas on Kangaroo Island and the mainland Mount Lofty Ranges in South Australia and found significant differences in vegetation structure important for Superb Fairy-wrens (percentage bare earth, shrub size and shrub abundance). Compared with mainland birds, island birds of both sexes: (1) occupied a wider niche breadth; (2) were significantly larger in body-size; and (3) varied less in morphology. Between the sexes: (1) there were few inter-sexual foraging differences; (2) males had a larger body-size and bill-length at both island and mainland locations; and (3) females had larger bill-width and bill-depth at both locations. These findings support the hypothesis of adaptive divergence in this species, with evidence that vegetation structure is important in their foraging behaviour and affects their morphology across locations (niche breadth was potentially favoured by a different interspecific community). The lack of consistent sexual differences in foraging ecology suggests that the patterns of sexual dimorphism may be shaped by reproductive roles rather than vegetation structure in this species. The categorisation of the Kangaroo Island population as a separate subspecies (M. c. ashbyi) is supported by these findings.
Analysis of anthocyanins and carotenoids in two varieties ofcalendula officinalisL. flowers

Pot Marigold (Calendula officinalis L.) is an annual erect herb with hispidly pubescent, corymbosely branched stem cultivated in lawns. The present investigation was carried out to study the dye yielding potential of the two varieties of Pot Marigold (Calendula officinalis L. var. Gitana Orange and Gitana Yellow) of Kashmir valley. The stability and color quality of pigments (anthocyanins and carotenoids) were assessed by quantifying the pigments and recording their color quality at 10 days interval at 0, 10, 30, 40, 50, 60, 70, 80 and 90 days after collection under ambient and refrigerated storage conditions. Results revealed that Pot marigold (var. Gitana Orange) had higher carotenoid content (288.33 mg/100g) than the Pot marigold (var. Gitana Yellow) (205.50 mg/100g). Highest pigment content was recorded during 0 days of storage in both the varieties. With increase in days of storage pigment content decreased in both plant material as well as extract under both storage conditions. Pigments in the plant material and extract stored under refrigerated conditions lasted longer than those stored under ambient conditions. Pigment degradation was more in the plant material as compared to the plant extract. Color quality of the plant species changed with increase in days of storage. From the present study it was concluded that both varieties of Pot Marigold have good levels of total carotenoids, thus petals of both varieties can be used as a raw material for extraction of yellow to orange natural dyes.
Gradient Hard Thresholding Pursuit

Hard Thresholding Pursuit (HTP) is an iterative greedy selection procedure for ﬁnding sparse solutions of underdetermined linear systems. This method has been shown to have strong theoretical guarantee and impressive numerical performance. In this article, we generalize HTP from compressed sensing to a generic problem setup of sparsity-constrained convex optimization. The proposed algorithm iterates between a standard gradient descent step and a hard-thresholding step with or without debiasing. We analyze the parameter estimation and sparsity recovery performance of the proposed method. Extensive numerical results conﬁrm our theoretical predictions and demonstrate the superiority of our method to the state-of-the-art greedy selection methods in sparse linear regression, sparse logistic regression and sparse precision matrix estimation problems. 1
Dyna Planning using a Feature Based Generative Model

Dyna-style reinforcement learning is a powerful approach for problems where not much real data is available. The main idea is to supplement real trajectories, or sequences of sampled states over time, with simulated ones sampled from a learned model of the environment. However, in large state spaces, the problem of learning a good generative model of the environment has been open so far. We propose to use deep belief networks to learn an environment model for use in Dyna. We present our approach and validate it empirically on problems where the state observations consist of images. Our results demonstrate that using deep belief networks, which are full generative models, significantly outperforms the use of linear expectation models, proposed in Sutton et al. (2008)
Sequential Observations of Conversion from Nonischemic to Ischemic Central Retinal Vein Occlusion Using Optical Coherence Tomography Angiography

We report the sequential changes of retinal vessels observed by optical coherence tomography angiography (OCTA) in a case of nonischemic central retinal vein occlusion (CRVO) that converted to ischemic CRVO. An 81-year-old woman visited our Retina Clinic because of visual acuity loss in the left eye. Funduscopic examination showed venous tortuosity and intraretinal hemorrhage in all four quadrants of the fundus. OCT showed macular edema. Fluorescein angiography (FA) and OCTA showed loss of small capillaries. Nonischemic CRVO was diagnosed. Antivascular endothelial growth factor (VEGF) treatment resolved the edema and improved visual acuity. However, during follow-up, capillary dropout was observed on OCTA, which gradually enlarged. Eventually, FA confirmed the conversion to ischemic CRVO. In this case, sequential observations using OCTA showed that nonischemic CRVO did not convert to ischemic CRVO abruptly but occurred stepwise. Additionally, vascular changes began around the veins and blood flow changes were observed more clearly in deep capillary plexus than in superficial capillary plexus.
The Absent in Melanoma 2-Like Receptor IFN-Inducible Protein 16 as an Inflammasome Regulator in Systemic Lupus Erythematosus: The Dark Side of Sensing Microbes

Absent in melanoma 2 (AIM2)-like receptors (ALRs) are a newly characterized class of pathogen recognition receptors (PRRs) involved in cytosolic and nuclear pathogen DNA recognition. In recent years, two ALR family members, the interferon (IFN)-inducible protein 16 (IFI16) and AIM2, have been linked to the pathogenesis of various autoimmune diseases, among which systemic lupus erythematosus (SLE) has recently gained increasing attention. SLE patients are indeed often characterized by constitutively high serum IFN levels and increased expression of IFN-stimulated genes due to an abnormal response to pathogens and/or incorrect self-DNA recognition process. Consistently, we and others have shown that IFI16 is overexpressed in a wide range of autoimmune diseases where it triggers production of specific autoantibodies. In addition, evidence from mouse models supports a model whereby ALRs are required for IFN-mediated host response to both exogenous and endogenous DNA. Following interaction with cytoplasmic or nuclear nucleic acids, ALRs can form a functional inflammasome through association with the adaptor ASC [apoptosis-associated speck-like protein containing a caspase recruitment domain (CARD)] and with procaspase-1. Importantly, inflammasome-mediated upregulation of IL-1β and IL-18 production positively correlates with SLE disease severity. Therefore, targeting ALR sensors and their downstream pathways represents a promising alternative therapeutic approach for SLE and other systemic autoimmune diseases.
Monitoring the hepatitis C care cascade using administrative claims data.

OBJECTIVES With the availability of curative therapies, it is important to ensure that individuals infected with hepatitis C virus (HCV) receive recommended testing, care, and treatment. We sought to evaluate insurance claims data as a source for monitoring progression along the HCV care cascade. STUDY DESIGN Longitudinal evaluation of disease progression, from diagnosis to treatment, among commercially insured enrollees with chronic HCV. METHODS We validated and used algorithms derived from standardized procedure and diagnosis codes to identify enrollees with chronic HCV in large insurance claims databases to describe the HCV care cascade, including the proportion engaged in HCV-specific care (13 possible definitions), the proportion prescribed HCV treatment, and the proportion who received an HCV RNA test 30 or more days after initiating treatment. RESULTS Approximately 90% of individuals with an HCV RNA test procedure code followed by either 3 or more chronic HCV diagnosis codes on different service dates or 2 or more chronic HCV diagnosis codes separated by more than 60 days truly had chronic HCV. Using these algorithms, we identified 5791 HCV cases from January 1, 2013, to June 30, 2014. Among enrollees with HCV, 95% were engaged in HCV care, but only 49% initiated treatment and 43% received a follow-up HCV RNA test 30 or more days after initiating treatment. CONCLUSIONS With validated case-finding algorithms, insurance claims data can be used to describe and monitor portions of the HCV care cascade. Although nearly all enrollees with HCV were engaged in HCV care, only half received treatment, indicating that even commercially insured enrollees may find it challenging to access treatment.
Partially Overlapping Brain Networks for Singing and Cello Playing

This research uses an MR-Compatible cello to compare functional brain activation during singing and cello playing within the same individuals to determine the extent to which arbitrary auditory-motor associations, like those required to play the cello, co-opt functional brain networks that evolved for singing. Musical instrument playing and singing both require highly specific associations between sounds and movements. However, vocal motor control is an evolutionarily old human trait and the auditory-motor associations used for singing are also used for speech and nonspeech vocalizations. This sets it apart from the arbitrary auditory-motor associations required to play musical instruments. The pitch range of the cello is similar to that of the human voice, but cello playing is completely independent of the vocal apparatus and can therefore be used to dissociate the auditory-vocal network from that of the auditory-motor network. While in the MR-Scanner, 11 expert cellists listened to and subsequently produced individual tones either by singing or cello playing. All participants were able to sing and play the target tones in tune (within 50Cents). We found that brain activity during cello playing directly overlaps with brain activity during singing in many areas within the auditory-vocal network. These include primary motor, dorsal pre-motor, and supplementary motor cortices, the primary and periprimary auditory cortices within the superior temporal gyrus including Heschl’s gyrus, anterior insula, anterior cingulate cortex, and intraparietal sulcus, and cerebellum but, notably, exclude the periaqueductal grey and basal ganglia. Second, we found that activity within the overlapping areas is positively correlated with, and therefore likely contributing to, both singing and playing in tune determined with performance measures. Third, we found that activity in auditory areas is functionally connected with activity in dorsal motor and pre-motor areas, and that the connectivity between them is positively correlated with good performance on this task. This functional connectivity suggests that the brain areas are working together to contribute to task performance and not just coincidently active. Last, our findings showed that cello playing may directly co-opt vocal areas (including larynx area of motor cortex), especially if musical training begins before age 7.
Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective

The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking.