Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of abomasally infused amylase and increasing amounts of corn starch on fecal excretion of starch, total and microbial nitrogen, and volatile fatty acids in heifers.

The aim of the present study was to study the effect of exogenous amylase on postruminal disappearance of increasing amounts of corn starch being infused into the abomasum of heifers, and to detect a possible limitation of starch digestion in the small intestine. Four rumen-fistulated heifers (two German Black Pied and two Jersey × German Black Pied) with an initial BW of 565 ± 6 kg were fed 5.6 kg DM/d of a diet targeted to contain only a negligible amount of starch. Animals were assigned randomly to a cross-over trial with two experimental periods lasting 35 d each with 10 d of diet adaption followed by 25 d of sample collection. During the sampling period, each animal was abomasally infused with native corn starch at five levels (953, 1213, 1425, 1733 and 1993 g DM/d) each for a 5-d period with and without exogenous amylase, respectively. At day 6 to 10 the heifers received an abomasal infusion of starch in amounts of 724 g/d. Feces were sampled four times a day during the collection periods. Titanium dioxide was ruminally administered (10 g/d) to estimate fecal excretion. Purine bases in feces were determined and used as a marker for microbial N excretion. Fecal excretion of microbial N increased linearly with increasing level of starch infusion (P < 0.001), indicating a constant proportion of the infused starch being fermented in the hindgut. In contrast, the apparent digestibility of starch from the total postruminal tract decreased linearly from 90 to 80% (P < 0.001) when the intestinal starch supply increased from 1 to 2 kg/d. There is strong evidence based on the increasing starch excretion with feces and the indication of a constant proportion of infused starch being fermented in the hindgut for a decreasing efficiency of starch digestion in the small intestine with increasing intestinal supply. Amylase administration increased fecal excretion of butyrate (P = 0.04) and tended to increase isovalerate excretion (P = 0.06). However, amylase did not affect fecal excretion of microbial N or starch, suggesting that pancreatic amylase activity may not be the primarily limiting factor of postruminal starch digestion in heifers when corn starch is abomasally infused in amounts up to 2 kg/d.
GemC1 is a critical switch for neural stem cell generation in the postnatal brain

The subventricular zone (SVZ) is one of two main niches where neurogenesis persists during adulthood, as it retains neural stem cells (NSCs) with self‐renewal capacity and multi‐lineage potency. Another critical cellular component of the niche is the population of postmitotic multiciliated ependymal cells. Both cell types are derived from radial glial cells that become specified to each lineage during embryogenesis. We show here that GemC1, encoding Geminin coiled‐coil domain‐containing protein 1, is associated with congenital hydrocephalus in humans and mice. Our results show that GemC1 deficiency drives cells toward a NSC phenotype, at the expense of multiciliated ependymal cell generation. The increased number of NSCs is accompanied by increased levels of proliferation and neurogenesis in the postnatal SVZ. Finally, GemC1‐knockout cells display altered chromatin organization at multiple loci, further supporting a NSC identity. Together, these findings suggest that GemC1 regulates the balance between NSC generation and ependymal cell differentiation, with implications for the pathogenesis of human congenital hydrocephalus.
Physiological model using diffuse reflectance spectroscopy for nonmelanoma skin cancer diagnosis

Diffuse reflectance spectroscopy (DRS) is a noninvasive, fast, and low‐cost technology with potential to assist cancer diagnosis. The goal of this study was to test the capability of our physiological model, a computational Monte Carlo lookup table inverse model, for nonmelanoma skin cancer diagnosis. We applied this model on a clinical DRS dataset to extract scattering parameters, blood volume fraction, oxygen saturation and vessel radius. We found that the model was able to capture physiological information relevant to skin cancer. We used the extracted parameters to classify (basal cell carcinoma [BCC], squamous cell carcinoma [SCC]) vs actinic keratosis (AK) and (BCC, SCC, AK) vs normal. The area under the receiver operating characteristic curve achieved by the classifiers trained on the parameters extracted using the physiological model is comparable to that of classifiers trained on features extracted via Principal Component Analysis. Our findings suggest that DRS can reveal physiologic characteristics of skin and this physiologic model offers greater flexibility for diagnosing skin cancer than a pure statistical analysis. Physiological parameters extracted from diffuse reflectance spectra data for nonmelanoma skin cancer diagnosis.
Case-matched comparison of postoperative outcomes following surgery for inflammatory bowel disease after exposure to vedolizumab vs. other biologics.

BACKGROUND AND AIM The effects of vedolizumab (VEDO) exposure on perioperative outcomes following surgery for inflammatory bowel disease (IBD) remain controversial. The aim of our study was to compare postoperative morbidity of IBD surgery following treatment with VEDO vs. other biologics or no biologics. METHODS An institutional, IRB-approved, prospectively-collected database was queried to identify all patients undergoing abdominal surgery for IBD between 8/2012 and 5/2017. The impact of VEDO within 12 weeks preoperatively on postoperative morbidity was initially assessed with univariate and multivariable analyses on all patients. A case-matched analysis was then carried out comparing patients exposed to VEDO vs. other biologic agents based on gender, age ± 5 years, diagnosis, date of surgery ± 2 years, and surgical procedure. RESULTS Out of 980 patients, 141 received VEDO. The majority of patients (59%) underwent surgery involving end or diverting ostomy creation. The initial multivariate analysis conducted on all patients indicated that VEDO use was independently associated with increased overall morbidity (p<0.001), but not infectious morbidity (p=0.30). However, the case-matched comparison of 95 VEDO-treated patients vs. 95 patients treated with adalimumab or infliximab did not indicate any difference in overall morbidity (p=0.32), infectious complications (p=0.15), or surgical site infections (p=0.12). CONCLUSIONS In a study population having a high rate of surgery involving ostomy creation, the exposure to preoperative VEDO was not associated with an increased morbidity rate when compared with other biologics.
Fast and low‐cost direct ELISA for high‐throughput serological HPA‐1a typing

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is caused by maternal alloantibodies against fetal human platelet antigens (HPAs), mostly caused by anti‐HPA‐1a. Population‐based screening for FNAIT is still a topic of debate. Logistically and financially, the major challenge for implementation is the typing of pregnant women to recognize the 2% HPA‐1a‐negative women. Therefore, there is need for a high‐throughput and low‐cost HPA‐1a‐typing assay.
Long-Term Survival after Acute Myocardial Infarction in Lithuania during Transitional Period (1996–2015): Data from Population-Based Kaunas Ischemic Heart Disease Register

Background and Objective: There is a lack of reliable epidemiological data on the long-term survival after acute myocardial infarction (AMI) in the Lithuanian population. The aim of the study was to evaluate the long-term (36 months) survival after AMI among persons aged 25–64 years, who had experienced AMI in four time-periods 1996, 2003–2004, 2008, and 2012. Material and Methods: The source of the data was Kaunas population-based Ischemic heart disease (IHD) register. Long-term survival after AMI (36 months) was evaluated using the Kaplan–Meier method. The survival curves significantly differed when p < 0.05. Hazard ratio for all-cause mortality and their 95% CIs, adjusted for baseline characteristics, were estimated with the Cox proportional hazards regression model. Results: The analysis of data on 36 months long-term survival among Kaunas population by sex and age groups showed that the survival rates among men and women were 83.4% and 87.6%, respectively (p < 0.05) and among 25–54 years-old and 55–64 years-old persons, 89.2% and 81.7%, respectively (p < 0.05). The rates of long-term survival of post-AMI Kaunas population were better in past periods than in first period. According to the data of the Kaplan-Meier survival analysis, long-term survival of 25 to 64-year-old post-AMI Kaunas population was without significantly difference in 1996, 2003–2004, 2008 and 2012 (Log-rank = 6.736, p = 0.081). The adjusted risk of all-cause mortality during 36 months among men and 25 to 54-year-old patients was on the average by 35% and 60% lower in 2012 than in 1996, respectively. Conclusion: It was found that 36 months survival post MI among women and younger (25–54 years) persons was significant better compared to men and older (55–64 years) persons. Long-term survival among 55 to 64-year-old post-AMI Kaunas population had a tendency to decrease during last period, while among 25–54 years old persons long-term survival was without significant changes. The results highlight the fact that AMI survivors, especially in youngest age, remain a high-risk group and reinforce the importance of primary and secondary prevention for the improvement of long-term prognosis of AMI patients.
Progressive fibrosing interstitial lung diseases: current practice in diagnosis and management

Abstract Objective: Some patients with interstitial lung diseases (ILDs) other than idiopathic pulmonary fibrosis (IPF) develop a progressive fibrosing phenotype. We investigated the diagnosis and management of non-IPF ILDs using data from a survey of physicians and from US insurance claims. Methods: Pulmonologists, rheumatologists and internists in France, Germany, Italy, Japan, Spain, UK and US who had managed ≥10 patients with non-IPF ILDs in the past year, including those with progressive fibrosing ILDs, completed an online survey. Data on US insurance and prescription claims were obtained from a repository that aggregates data on claims routed from providers or pharmacies to payers. Results: In May–June 2017, 243 pulmonologists, 203 rheumatologists and 40 internists completed an online survey. Respondents estimated that 18–32% of patients diagnosed with non-IPF ILDs develop progressive fibrosis and that time from symptom onset to death in these patients was 61–80 months. Drug treatment was given to 50–75% of patients with non-IPF progressive fibrosing ILDs. Reasons for patients not being treated included that physicians considered patients to have mild or slowly progressing disease, or did not believe that available treatments are effective or well tolerated. Corticosteroids were the preferred first-line treatment for all types of non-IPF ILD. There was considerable heterogeneity in preferences for second- and third-line treatments. US insurance claims data from 3823 patients indicated that, in 2016, 50–75% of patients with ILDs received drug treatment (mostly corticosteroids) for their ILD. Conclusions: Physicians estimate that 18–32% of patients diagnosed with non-IPF ILDs develop a progressive fibrosing phenotype and that these patients experience significant delays in the diagnosis of ILD and the detection of progressive fibrosis. Between 25% and 50% of patients with progressive fibrosing ILDs do not receive drug therapy. There is an unmet need for effective and well tolerated treatments for progressive fibrosing ILDs.
Delay in development and behavioural abnormalities in the absence of p53 in zebrafish

p53 is well-known for its tumour-suppressive activity. However, in the past decade it became clear that p53 is also involved in other processes including stem cell proliferation, differentiation and animal development. To investigate the role of p53 in early embryonic development, we targeted p53 by CRISPR/Cas9 to make a p53 knock-out zebrafish (Danio rerio). Our data show developmental and behavioural effects in p53-deficient zebrafish embryos and larvae. Specifically, we found that early development of zebrafish was clearly delayed in the absence of p53. However, after 1 day (1 dpf), the p53-deficient embryos appeared to recover, as evidenced by a similar level of pigmentation at 26 hpf, similar size of the eye at 4 dpf and only a minor difference in body size at 4 dpf compared to p53 wild-type siblings. The recovery of development after 1 dpf in p53-deficient embryos could be due to a compensatory mechanism involving other p53 family members. p63 and p73 were found over-expressed with respect to wild-type siblings. However, despite this adaptation, the hatching time remained delayed in p53-/- zebrafish. In addition to differences in development, p53-null zebrafish embryos also showed differences in behaviour. We observed an overall reduced activity and a reduced travel distance under non-stressed conditions and after exposing the larvae to vibration. We also observed a longer latency until the larvae started to move after touching with a needle. Overall, these data indicate that p53 is involved in early development and locomotion activities.
Barrier Access Control Using Sensors Platform and Vehicle License Plate Characters Recognition

The paper proposes a sensors platform to control a barrier that is installed for vehicles entrance. This platform is automatized by image-based license plate recognition of the vehicle. However, in situations where standardized license plates are not used, such image-based recognition becomes non-trivial and challenging due to the variations in license plate background, fonts and deformations. The proposed method first detects the approaching vehicle via ultrasonic sensors and, at the same time, captures its image via a camera installed along with the barrier. From this image, the license plate is automatically extracted and further processed to segment the license plate characters. Finally, these characters are recognized with the help of a standard optical character recognition (OCR) pipeline. The evaluation of the proposed system shows an accuracy of 98% for license plates extraction, 96% for character segmentation and 93% for character recognition.
Accuracy Analysis in Sensor Networks for Asynchronous Positioning Methods

The accuracy requirements for sensor network positioning have grown over the last few years due to the high precision demanded in activities related with vehicles and robots. Such systems involve a wide range of specifications which must be met through positioning devices based on time measurement. These systems have been traditionally designed with the synchronization of their sensors in order to compute the position estimation. However, this synchronization introduces an error in the time determination which can be avoided through the centralization of the measurements in a single clock in a coordinate sensor. This can be found in typical architectures such as Asynchronous Time Difference of Arrival (A-TDOA) and Difference-Time Difference of Arrival (D-TDOA) systems. In this paper, a study of the suitability of these new systems based on a Cramér-Rao Lower Bound (CRLB) evaluation was performed for the first time under different 3D real environments for multiple sensor locations. The analysis was carried out through a new heteroscedastic noise variance modelling with a distance-dependent Log-normal path loss propagation model. Results showed that A-TDOA provided less uncertainty in the root mean square error (RMSE) in the positioning, while D-TDOA reduced the standard deviation and increased stability all over the domain.
The collectivity of British alcohol consumption trends across different temporal processes: A quantile age-period-cohort analysis.

BACKGROUND AND AIMS UK alcohol consumption per capita has fallen by 18% since 2004 while the alcohol-specific death rate has risen by 6%. Inconsistent consumption trends across the population may explain this. Drawing on the theory of the collectivity of drinking cultures and age-period-cohort analyses, we tested whether consumption trends are consistent across lighter and heavier drinkers for three temporal processes: (i) the life course, (ii) calendar time, (iii) successive birth cohorts. DESIGN Sex-specific quantile age-period-cohort regressions using repeat cross-sectional survey data. SETTING Great Britain, 1984-2011. PARTICIPANTS Adult (18+) drinkers responding to 17 waves of the General Lifestyle Survey (total N=175,986). MEASUREMENTS Dependent variable: The 10th , 25th , 50th , 75th , 90th , 95th and 99th quantiles of the logged weekly alcohol consumption distribution (excluding abstainers). INDEPENDENT VARIABLES seven age groups (18-24, 25-34 … 65-74, 75+), five time periods (1984-1988 … 2002-2006, 2008-2011) and 16 five-year birth cohorts (1915-1919 … 1990-1994). Additional control variables: ethnicity and UK country. FINDINGS Within age, period and cohort trends, changes in consumption were not consistently in the same direction at different quantiles of the consumption distribution. When they were, the scale of change sometimes differed between quantiles. For example, consumption among women decreased by 18% (CI95: -32% - -2%) but increased by 11% (CI95: 2% - 21%) at the median and by 28% (CI95: 19%-38%) at the 99th quantile, implying consumption fell among lighter drinkers and rose among heavier drinkers. This type of polarised trend also occurred between 1984-1988 and 1996-2000 for men and women. Age trends showed collectivity but cohort trends showed a mixture of collectivity and polarisation. CONCLUSIONS Countervailing alcohol consumption and alcohol-related harm trends in the UK may be explained by lighter and heavier drinkers having different period and cohort trends as well as by the presence of cohort trends that mean consumption may rise in some age groups while falling in others.
Automating machine learning

© Springer International Publishing AG 2016. I will describe the “Automatic Statistician”1, a project which aims to automate the exploratory analysis and modelling of data. Our approach starts by defining a large space of related probabilistic models via a grammar over models, and then uses Bayesian marginal likelihood computations to search over this space for one or a few good models of the data. The aim is to find models which have both good predictive performance, and are somewhat interpretable. The Automatic Statistician generates a natural language summary of the analysis, producing a 10‒15 page report with plots and tables describing the analysis. I will also link this to recent work we have been doing in the area of Probabilistic Programming (including an new system in Julia) to automate inference, and on the rational allocation of computational resources (and our entry in the AutoML conference).
Children’s DAT1 Polymorphism Moderates the Relationship Between Parents’ Psychological Profiles, Children’s DAT Methylation, and Their Emotional/Behavioral Functioning in a Normative Sample

Parental psychopathological risk is considered as one of the most crucial features associated with epigenetic modifications in offspring, which in turn are thought to be related to their emotional/behavioral profiles. The dopamine active transporter (DAT) gene is suggested to play a significant role in affective/behavioral regulation. On the basis of the previous literature, we aimed at verifying whether children’s DAT1 polymorphisms moderated the relationship between parents’ psychological profiles, children’s emotional/behavioral functioning, and DAT1 methylation in a normative sample of 79 families with school-age children (Ntot = 237). Children’s biological samples were collected through buccal swabs, while Symptom Check-List-90 item Revised, Adult Self Report, and Child Behavior Check-List/6–18 was administered to assess parental and children’s psychological functioning. We found that higher maternal externalizing problems predicted the following: higher levels of children’s DAT1 methylation at M1, but only among children with 10/10 genotype; higher levels of methylation at M2 among children with 10/10 genotype; while lower levels for children with a 9-repeat allele. There was also a positive relationship between fathers’ externalizing problems and children’s externalizing problems, only for children with a 9-repeat allele. Our findings support emerging evidence of the complex interplay between genetic and environmental factors in shaping children’ emotional/behavioral functioning, contributing to the knowledge of risk variables for a child’s development and psychological well-being.
'Please sort these voice recordings into 2 identities': Effects of task instructions on performance in voice sorting studies.

We investigated the effects of two types of task instructions on performance on a voice sorting task by listeners who were either familiar or unfamiliar with the voices. Listeners were asked to sort 15 naturally varying stimuli from two voice identities into perceived identities. Half of the listeners sorted the recordings freely into as many identities as they perceived; the other half were forced to sort stimuli into two identities only. As reported in previous studies, unfamiliar listeners formed more clusters than familiar listeners. Listeners therefore perceived different naturally varying stimuli from the same identity as coming from different identities, while being highly accurate at telling apart the stimuli from different voices. We further show that a change in task instructions - forcing listeners to sort stimuli into two identities only - helped unfamiliar listeners to overcome this selective failure at 'telling people together'. This improvement, however, came at the cost of an increase in errors in telling people apart. For familiar listeners, similar non-significant trends were apparent. Therefore, even when informed about correct number of identities, listeners may fail to accurately perceive identity further highlighting that voice identity perception in the context of natural within-person variability is a challenging task. We discuss our results in terms of similarities and differences to findings in the face perception literature and their importance in applied settings, such as forensic voice identification.
The price of privilege: helping mom die at home

Abstract Americans overwhelmingly wish to age in place and many explicitly want to die at home. Yet, the anemic welfare state means that only the most fortunate among us are able to achieve that goal. A disproportionate burden of care falls squarely to families, which are smaller and more geographically spread out than ever before. Carers too often wind up in environments that are far from conducive, namely being older and perhaps frail themselves or younger and perhaps with small children of their own. Drawing on an autoethnographic study of my mother’s final years and a case study analysis of one innovative home care agency, this project examines the individual and organizational factors that allow one family to grant their family member’s wish to die at home. Grounded theory methods revealed facilitators including presence of a home-based long term care insurance policy, geographic mobility, and access to a democratically-oriented home care organization. Barriers, of course, include lack of access to long term care insurance and a daughter who lives in a progressive state with a waiver for Home and Community Based Services. While the privilege of access underscores the social determinants of aging, this case study reveals some important features that suggest how senior social services could be. Even for the “ideal type” presented here, the many trials and tribulations of aiding a loved one to die at home relate to the untenable nature of doing it all in a context whereby social services are fragmented and driven by financial incentives.