Miracle-dz/UniFAR-FTUs huggingface dataset:
The enemy of my enemy is my friend: native pine marten recovery reverses the decline of the red squirrel by suppressing grey squirrel populations

Shared enemies may instigate or modify competitive interactions between species. The dis-equilibrium caused by non-native species introductions has revealed that the outcome of such indirect interactions can often be dramatic. However, studies of enemy-mediated competition mostly consider the impact of a single enemy, despite species being embedded in complex networks of interactions. Here, we demonstrate that native red and invasive grey squirrels in Britain, two terrestrial species linked by resource and disease-mediated apparent competition, are also now linked by a second enemy-mediated relationship involving a shared native predator recovering from historical persecution, the European pine marten. Through combining spatial capture–recapture techniques to estimate pine marten density, and squirrel site-occupancy data, we find that the impact of exposure to predation is highly asymmetrical, with non-native grey squirrel occupancy strongly negatively affected by exposure to pine martens. By contrast, exposure to pine marten predation has an indirect positive effect on red squirrel populations. Pine marten predation thus reverses the well-documented outcome of resource and apparent competition between red and grey squirrels.
Colorectal polyp segmentation using a fully convolutional neural network

Colorectal cancer is the third common cancer in the United States and most colorectal cancer is associated with colorectal polyps. In hospital, colonoscopy is a common way to detect colorectal polyps. Colorectal polyps segmentation plays an important role in the diagnosis and prevention of digestive system related diseases. Therefore, there is a pressure-need for polyp segmentation computer-aided system to help doctors in diagnosis. In this paper, we propose a new, end-to-end fully convolutional neural network structure for segmenting colorectal polyps. This method can directly output a prediction map of the same size as the original image of the input network. We use the CVC-ClinicDB database to evaluate our method. Proposed method achieves accuracy values of 96.98%, F1score values of 83.01%, sensitivity values of 77.32% and specificity values of 99.05%.
Biochemistry of complex glycan depolymerisation by the human gut microbiota

&NA; The human gut microbiota (HGM) makes an important contribution to health and disease. It is a complex microbial community of trillions of microbes with a majority of its members represented within two phyla, the Bacteroidetes and Firmicutes, although it also contains species of Actinobacteria and Proteobacteria. Reflecting its importance, the HGM is sometimes referred to as an ‘organ' as it performs functions analogous to systemic tissues within the human host. The major nutrients available to the HGM are host and dietary complex carbohydrates. To utilise these nutrient sources, the HGM has developed elaborate, variable and sophisticated systems for the sensing, capture and utilisation of these glycans. Understanding nutrient acquisition by the HGM can thus provide mechanistic insights into the dynamics of this ecosystem, and how it impacts human health. Dietary nutrient sources include a wide variety of simple and complex plant and animal‐derived glycans most of which are not degraded by enzymes in the digestive tract of the host. Here we review how various adaptive mechanisms that operate across the major phyla of the HGM contribute to glycan utilisation, focusing on the most complex carbohydrates presented to this ecosystem.
Constraint-Induced Aphasia Therapy in the Acute Stage

Background. Constraint-induced aphasia therapy (CIAT) has proven effective in patients with subacute and chronic forms of aphasia. It has remained unclear, however, whether intensity of therapy or constraint is the relevant factor. Data about intensive speech and language therapy (SLT) are conflicting. Objective. To identify the effective component of CIAT and assess the feasibility of SLT in the acute stage after stroke. Method. A total of 60 patients with aphasia (68.2 ± 11.7 years) were enrolled 18.9 days after first-ever stroke. They were randomly distributed into 3 groups: (1) CIAT group receiving therapy for 3 hours per day (10 workdays, total 30 hours); (2) conventional communication treatment group, with same intensity without constraints; and (3) control group receiving individual therapy twice a day as well as group therapy (total 14 hours). Patients were assessed pretreatment and posttreatment using the Aachener Aphasia Test (primary end point: token test) and the Communicative Activity Log (CAL). Results. Pretreatment, there were no between-group differences. Posttreatment, all groups showed significant improvements without between-group differences. Conclusion. It was found that 14 hours of aphasia therapy administered within 2 weeks as individual therapy, focusing on individual deficits, combined with group sessions has proven to be most efficient. This approach yielded the same outcome as 30 hours of group therapy, either in the form of CIAT or group therapy without constraints. SLT in an intensive treatment schedule is feasible and was well tolerated in the acute stage after stroke.
"Haru": Hardware Design of an Experimental Tabletop Robot Assistant

This paper discusses the design and development of an experimental tabletop robot called "Haru" based on Design Thinking methodology. Right from the very beginning of the design process, we have brought an interdisciplinary team that includes animators, performers and sketch artists to help create the first iteration of a distinctive anthropomorphic robot design based on a concept that leverages form factor with functionality. Its unassuming physical affordance is intended to keep human expectation grounded while its actual interactive potential stokes human interest. The meticulous combination of both subtle and pronounced mechanical movements together with its stunning visual displays, highlight its affective affordance. As a result, we have developed the first iteration of our tabletop robot rich in affective potential for use in different research fields involving long-term human-robot interaction.
Telomere biology and age-related diseases

Abstract Telomeres are the protective end caps of chromosomes and shorten with every cell division. Telomere length has been proposed as a biomarker of biological age and a risk factor for age-related diseases. Epidemiologic studies show an association between leukocyte telomere length (LTL) and mortality. There is solid evidence that links LTL with cardiovascular disease. Short telomeres promote atherosclerosis and impair the repair of vascular lesions. Alzheimer’s disease patients have also a reduced LTL. Telomeres measured in tumor tissue from breast, colon and prostate are shorter than in healthy tissue from the same organ and the same patient. In healthy tissue directly adjacent to these tumors, telomeres are also shorter than in cells that are more distant from the cancerous lesion. A reduced telomere length in cancer tissue from breast, colon and prostate is associated with an advanced disease state at diagnosis, faster disease progression and poorer survival. By contrast, results regarding LTL and cancer are inconsistent. Furthermore, the majority of studies did not find significant associations between LTL, bone mineral density (BMD) and osteoporosis. The present manuscript gives an overview about our current understanding of telomere biology and reviews existing knowledge regarding the relationship between telomere length and age-related diseases.
Adjuvant endocrine therapy after breast cancer: a qualitative study of factors associated with adherence

Introduction Despite evidence of the efficacy of adjuvant endocrine therapy (AET) in reducing the risk of recurrence and mortality after treatment for primary breast cancer, adherence to AET is suboptimal. This study aimed to explore factors that influence adherence and nonadherence to AET following breast cancer to inform the development of supportive interventions. Methods Interviews were conducted with 32 women who had been prescribed AET, 2–4 years following their diagnosis of breast cancer. Both adherers (n=19) and nonadherers (n=13) were recruited. The analysis was conducted using the Framework approach. Results Factors associated with adherence were as follows: managing side effects including information and advice on side effects and taking control of side effects, supportive relationships, and personal influences. Factors associated with nonadherence were as follows: burden of side effects, feeling unsupported, concerns about long-term AET use, regaining normality, including valuing the quality of life over length of life, and risk perception. Conclusion Provision of timely information to prepare women for the potential side effects of AET and education on medication management strategies are needed, including provision of timely and accurate information on the efficacy of AET in reducing breast cancer recurrence and on potential side effects and ways to manage these should they arise. Trust in the doctor–patient relationship and clear patient pathways for bothersome side effects and concerns with AET are important. Training and education on AET for GPs should be considered alongside novel care pathways such as primary care nurse cancer care review and community pharmacist follow-up.
Effect of mobile technology featuring visual scene displays and just-in-time programming on communication turns by preadolescent and adolescent beginning communicators

Abstract Purpose: Visual scene displays (VSDs) and just-in-time programming supports are augmentative and alternative communication (AAC) technology features with theoretical benefits for beginning communicators of all ages. The goal of the current study was to evaluate the effects of a communication application (app) on mobile technology that supported the just-in-time programming of VSDs on the communication of preadolescents and adolescents who were beginning communicators. Method: A single-subject multiple-baseline across participant design was employed to evaluate the effect of the AAC app with VSDs programmed just-in-time by the researcher on the communication turns expressed by five preadolescents and adolescents (9–18 years old) who were beginning communicators. Result: All five participants demonstrated marked increases in the frequency of their communication turns after the onset intervention. Conclusion: Just-in-time programming support and VSDs are two features that may positively impact communication for beginning communicators in preadolescence and adolescence. Apps with these features allow partners to quickly and easily capture photos of meaningful and motivating events and provide them immediately as VSDs with relevant vocabulary to support communication in response to beginning communicators’ interests.
Estimation of regional richness in marine benthic communities: quantifying the error

Species richness is the most widely used measure of biodiversity. It is considered crucial for testing numerous ecological theories. While local species richness is easily determined by sampling, the quantification of regional richness relies on more or less complete species inventories, expert estimation, or mathematical extrapolation from a number of replicated local samplings. However the accuracy of such extrapolations is rarely known. In this study, we compare the common estimators MM (Michaelis‐Menten), Chao1, Chao2, ACE (Abundance‐based Coverage Estimator), and the first and second order Jackknifes against the asymptote of the species accumulation curve, which we use as an estimate of true regional richness. Subsequently, we quantified the role of sample size, i.e., number of replicates, for precision, accuracy, and bias of the estimation. These replicates were sub‐sets of three large data sets of benthic assemblages from the NE Atlantic: (i) soft‐bottom sediment communities in the Western Baltic (n = 70); (ii) hard‐bottom communities from emergent rock on the Island of Helgoland, North Sea (n = 52), and (iii) hard‐bottom assemblages grown on artificial substrata in Madeira Island, Portugal (n = 56). For all community types, Jack2 showed a better performance in terms of bias and accuracy while MM exhibited the highest precision. However, in virtually all cases and across all sampling efforts, the estimators underestimated the regional species richness, regardless of habitat type, or selected estimator. Generally, the amount of underestimation decreased with sampling effort. A logarithmic function was applied to quantify the bias caused by low replication using the best estimator, Jack2. The bias was more obvious in the soft‐bottom environment, followed by the natural hard‐bottom and the artificial hard‐bottom habitats, respectively. If a weaker estimator in terms of performance is chosen for this quantification, more replicates are required to obtain a reliable estimation of regional richness.
The making of bispecific antibodies

ABSTRACT During the past two decades we have seen a phenomenal evolution of bispecific antibodies for therapeutic applications. The ‘zoo’ of bispecific antibodies is populated by many different species, comprising around 100 different formats, including small molecules composed solely of the antigen-binding sites of two antibodies, molecules with an IgG structure, and large complex molecules composed of different antigen-binding moieties often combined with dimerization modules. The application of sophisticated molecular design and genetic engineering has solved many of the technical problems associated with the formation of bispecific antibodies such as stability, solubility and other parameters that confer drug properties. These parameters may be summarized under the term ‘developability’. In addition, different ‘target product profiles’, i.e., desired features of the bispecific antibody to be generated, mandates the need for access to a diverse panel of formats. These may vary in size, arrangement, valencies, flexibility and geometry of their binding modules, as well as in their distribution and pharmacokinetic properties. There is not ‘one best format’ for generating bispecific antibodies, and no single format is suitable for all, or even most of, the desired applications. Instead, the bispecific formats collectively serve as a valuable source of diversity that can be applied to the development of therapeutics for various indications. Here, a comprehensive overview of the different bispecific antibody formats is provided.
Indian Health Service Care System and Cancer Stage in American Indians and Alaska Natives

Abstract:Purpose. We aimed to determine whether the association between late-stage cancer and American Indian/Alaska Native (AI/AN) race differed by enrollment in the Indian Health Service Care System (IHSCS). Methods. We used Surveillance, Epidemiology, and End Results (SEER) data linked to Medicare files to compare the odds of late-stage breast, colorectal, lung, or prostate cancer between non-Hispanic Whites (NHWs) (n=285,993) and AI/ANs with (n=581) and without (n=543) IHSCS enrollment. Results. For AI/ANs without IHSCS enrollment, the odds of late-stage disease were higher in AI/ANs compared with NHWs for breast (OR=3.17, 95%CI: 1.82–5.53) and for prostate (OR=2.59, 95%CI:1.55–4.32) cancer, but not for colorectal or lung cancers. Among AI/ANs with IHSCS enrollment, there was not a significant association between late-stage disease and AI/AN race for any of the four cancers evaluated. Conclusion. Our results suggest that enrollment in the IHSCS reduced the disparity between AI/ANs and NHWs with respect to late-stage cancer diagnoses.
Affective symptoms and quality of life in patients with voiding or storage dysfunction: Results before and after sacral neuromodulation: A prospective follow‐up study

Sacral neuromodulation (SNM) is an effective treatment for patients with overactive bladder syndrome (OAB) or non‐obstructive urinary retention (NOR). These lower urinary tract symptoms (LUTS) are the result of a functional urological cause but often coincide with psychological and/or psychiatric factors. It has been stated that there is an association between LUTS, depression and anxiety disorders.
Neural circuits via which single prolonged stress exposure leads to fear extinction retention deficits

Single prolonged stress (SPS) has been used to examine mechanisms via which stress exposure leads to post-traumatic stress disorder symptoms. SPS induces fear extinction retention deficits, but neural circuits critical for mediating these deficits are unknown. To address this gap, we examined the effect of SPS on neural activity in brain regions critical for extinction retention (i.e., fear extinction circuit). These were the ventral hippocampus (vHipp), dorsal hippocampus (dHipp), basolateral amygdala (BLA), prelimbic cortex (PL), and infralimbic cortex (IL). SPS or control rats were fear conditioned then subjected to extinction training and testing. Subsets of rats were euthanized after extinction training, extinction testing, or immediate removal from the housing colony (baseline condition) to assay c-Fos levels (measure of neural activity) in respective brain region. SPS induced extinction retention deficits. During extinction training SPS disrupted enhanced IL neural activity and inhibited BLA neural activity. SPS also disrupted inhibited BLA and vHipp neural activity during extinction testing. Statistical analyses suggested that SPS disrupted functional connectivity within the dHipp during extinction training and increased functional connectivity between the BLA and vHipp during extinction testing. Our findings suggest that SPS induces extinction retention deficits by disrupting both excitatory and inhibitory changes in neural activity within the fear extinction circuit and inducing changes in functional connectivity within the Hipp and BLA.
Development of lifetime comorbidity in the World Health Organization world mental health surveys.

CONTEXT Although numerous studies have examined the role of latent variables in the structure of comorbidity among mental disorders, none has examined their role in the development of comorbidity. OBJECTIVE To study the role of latent variables in the development of comorbidity among 18 lifetime DSM-IV disorders in the World Health Organization World Mental Health Surveys. DESIGN Nationally or regionally representative community surveys. SETTING Fourteen countries. PARTICIPANTS A total of 21 229 survey respondents. MAIN OUTCOME MEASURES First onset of 18 lifetime DSM-IV anxiety, mood, behavior, and substance disorders assessed retrospectively in the World Health Organization Composite International Diagnostic Interview. RESULTS Separate internalizing (anxiety and mood disorders) and externalizing (behavior and substance disorders) factors were found in exploratory factor analysis of lifetime disorders. Consistently significant positive time-lagged associations were found in survival analyses for virtually all temporally primary lifetime disorders predicting subsequent onset of other disorders. Within-domain (ie, internalizing or externalizing) associations were generally stronger than between-domain associations. Most time-lagged associations were explained by a model that assumed the existence of mediating latent internalizing and externalizing variables. Specific phobia and obsessive-compulsive disorder (internalizing) and hyperactivity and oppositional defiant disorders (externalizing) were the most important predictors. A small number of residual associations remained significant after controlling the latent variables. CONCLUSIONS The good fit of the latent variable model suggests that common causal pathways account for most of the comorbidity among the disorders considered herein. These common pathways should be the focus of future research on the development of comorbidity, although several important pairwise associations that cannot be accounted for by latent variables also exist that warrant further focused study.
Summer upwelling at the Boknis Eck time series station (1982 to 2012) - a combined glider and wind data analysis

Two consecutive summer upwelling events, each lasting for less than 24 h, were surveyed in high temporal and vertical resolution close to the Boknis Eck time-series station (BE) in the western Belt Sea (Baltic Sea) in summer 2010 with an autonomous glider. Driven only by moderate offshore winds both events resulted in more than 5 K cooling of surface waters, while only for the second event were significant irreversible changes in the vertical stratification observed. Generalizing the glider survey observations with hourly wind data from nearby meteorological stations, it is found that upwelling in the BE area occurs for wind directions between 190 to 260° and wind speed exceeding 4 m s−1. Based on these thresholds the wind-induced summer (June to September) upwelling conditions in the BE area for the period 1982 to 2012 are reconstructed. On average about 18 days of upwelling favourable wind conditions are found for the four summer months, with significant interannual variability ranging from 7.7 days (2006) to more than 28 days (1985). By aligning upwelling favourable wind conditions with the monthly BE surveys it is found that extreme anomalies in BE surveys follow extended periods of upwelling favourable winds.
Loss-of-Function Mutations in HspR Rescue the Growth Defect of a Mycobacterium tuberculosis Proteasome Accessory Factor E (pafE) Mutant

ABSTRACT Mycobacterium tuberculosis uses a proteasome to degrade proteins by both ATP-dependent and -independent pathways. While much has been learned about ATP-dependent degradation, relatively little is understood about the ATP-independent pathway, which is controlled by Mycobacterium tuberculosisproteasome accessory factor E (PafE). Recently, we found that a Mycobacterium tuberculosispafE mutant has slowed growth in vitro and is sensitive to killing by heat stress. However, we did not know if these phenotypes were caused by an inability to degrade the PafE-proteasome substrate HspR (heat shock protein repressor), an inability to degrade any damaged or misfolded proteins, or a defect in another protein quality control pathway. To address this question, we characterized pafE suppressor mutants that grew similarly to pafE+ bacteria under normal culture conditions. All but one suppressor mutant analyzed contained mutations that inactivated HspR function, demonstrating that the slowed growth and heat shock sensitivity of a pafE mutant were caused primarily by the inability of the proteasome to degrade HspR. IMPORTANCE Mycobacterium tuberculosis encodes a proteasome that is highly similar to eukaryotic proteasomes and is required for virulence. We recently discovered a proteasome cofactor, PafE, which is required for the normal growth, heat shock resistance, and full virulence of M. tuberculosis. In this study, we demonstrate that PafE influences this phenotype primarily by promoting the expression of protein chaperone genes that are necessary for surviving proteotoxic stress.