Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of evolution of MHC class II genes of crows (Corvus) suggest trans-species polymorphism

A distinguishing characteristic of genes that code for the major histocompatibility complex (MHC) is that alleles often share more similarity between, rather than within species. There are two likely mechanisms that can explain this pattern: convergent evolution and trans-species polymorphism (TSP), in which ancient allelic lineages are maintained by balancing selection and retained by descendant species. Distinguishing between these two mechanisms has major implications in how we view adaptation of immune genes. In this study we analyzed exon 2 of the MHC class IIB in three passerine bird species in the genus Corvus: jungle crows (Corvus macrorhynchos japonensis) American crows (C. brachyrhynchos) and carrion crows (C. corone orientalis). Carrion crows and American crows are recently diverged, but allopatric, sister species, whereas carrion crows and jungle crows are more distantly related but sympatric species, and possibly share pathogens linked to MHC IIB polymorphisms. These patterns of evolutionary divergence and current geographic ranges enabled us to test for trans-species polymorphism and convergent evolution of the MHC IIB in crows. Phylogenetic reconstructions of MHC IIB sequences revealed several well supported interspecific clusters containing all three species, and there was no biased clustering of variants among the sympatric carrion crows and jungle crows. The topologies of phylogenetic trees constructed from putatively selected sites were remarkably different than those constructed from putatively neutral sites. In addition, trees constructed using non-synonymous substitutions from a continuous fragment of exon 2 had more, and generally more inclusive, supported interspecific MHC IIB variant clusters than those constructed from the same fragment using synonymous substitutions. These phylogenetic patterns suggest that recombination, especially gene conversion, has partially erased the signal of allelic ancestry in these species. While clustering of positively selected amino acids by supertyping revealed a single supertype shared by only jungle and carrion crows, a pattern consistent with convergence, the overall phylogenetic patterns we observed suggest that TSP, rather than convergence, explains the interspecific allelic similarity of MHC IIB genes in these species of crows.
Protein-Mediated Precipitation of Calcium Carbonate

Calcium carbonate is an important component in exoskeletons of many organisms. The synthesis of calcium carbonate was performed by mixing dimethyl carbonate and an aqueous solution of calcium chloride dihydrate. The precipitation product was characterized by means of scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) measurements. In addition, the turbidity of the reaction solution was acquired to monitor the kinetics of the calcium carbonate structure’s growth in the investigated system. In this study, samples of CaCO3 particles obtained with individual proteins, such as ovalbumin, lysozyme, and a mixture of the proteins, were characterized and compared with a control sample, i.e., synthesized without proteins. The obtained data indicated that the addition of ovalbumin to the reaction changed the morphology of crystals from rhombohedral to ‘stack-like’ structures. Lysozyme, however, did not affect the morphology of calcium carbonate, yet the presence of the protein mixture led to the creation of more complex composites in which the calcium carbonate crystals were constructed in protein matrices formed by the ovalbumin-lysozyme interaction. It was also observed that in the protein mixture, ovalbumin has a major influence on the CaCO3 formation through a strong interaction with calcium ions, which leads to the coalescence and creation of a steric barrier reducing particle growth. The authors proposed a mechanism of calcium carbonate grain growth in the presence of both proteins, taking into account the interaction of calcium ions with the protein.
Randomized Trial of Long-Acting Insulin Glargine Titration Web Tool (LTHome) Versus Enhanced Usual Therapy of Glargine Titration (INNOVATE Trial).

BACKGROUND Basal insulin titration in the real world is often unsuccessful. LTHome, a web tool, applies a rules engine-based algorithm providing insulin titration advice directly to the patient. METHODS This pilot, randomized trial evaluates basal insulin glargine titration by LTHome compared to enhanced usual therapy ([EUT]-diabetes education program) over 12 weeks. Important inclusion criteria: 18-75 years, type 2 diabetes, computer literacy, and HbA1c >7.0%. Trial protocol was approved by ethics board. RESULTS We randomized 139 subjects. The achievement of primary composite outcome (four out of seven fasting plasma glucose [FPG] within 5-7.2 mmol/L + mean for three consecutive FPG within 5-7.2 mmol/L + no severe hypoglycemia) was 15% in LTHome versus 41% in EUT (noninferiority not met, P-value = 0.92). Other outcomes were similar between the LTHome and EUT arms: alternate composite outcome achievement (last five FPG mean within the range of 5-7.2 mmol/L + no hypoglycemia, 47% and 51%, P = 0.73); A1c reduction (-1.0% and -1.1%, P = 0.66); proportion achieving A1c ≤7% (14% and 20%, P = 0.36); and hypoglycemia incidence (31% and 37%, P = 0.4), respectively. Patient satisfaction score improvements were greater in LTHome versus EUT (change in fear of hypoglycemia score P = 0.04 and change in diabetes distress score P = 0.04). The mean number of additional healthcare provider visits was 0.13 for LTHome and 1.22 for EUT (P < 0.01). CONCLUSION INNOVATE trial suggests clinical utility of LTHome compared to EUT in real-life settings. Further research is needed to evaluate the efficacy and safety of automated insulin titration algorithms.
Attribute-Based Classification for Zero-Shot Visual Object Categorization

—We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.
VC-Dimensions of Random Function Classes

For any class of binary functions on [n]={1, . , n} a classical result by Sauer states a sufficient condition for its VC-dimension to be at least d: its cardinality should be at least O(nd-1). A necessary condition is that its cardinality be at least 2d (which is O(1) with respect to n). How does the size of a 'typical' class of VC-dimension d compare to these two extreme thresholds ? To answer this, we consider classes generated randomly by two methods, repeated biased coin flips on the n-dimensional hypercube or uniform sampling over the space of all possible classes of cardinality k on [n]. As it turns out, the typical behavior of such classes is much more similar to the necessary condition; the cardinality k need only be larger than a threshold of 2d for its VC-dimension to be at least d with high probability. If its expected size is greater than a threshold of O(ln) (which is still significantly smaller than the sufficient size of O(nd-1)) then it shatters every set of size d with high probability. The behavior in the neighborhood of these thresholds is described by the asymptotic probability distribution of the VC-dimension and of the largest d such that all sets of size d are shattered.
The effect of visual barriers, outdoor housing and feeding enrichment on the behaviour of drills (Mandrillus leucophaeus) at Parken Zoo

Animals are confronted with potential stressors at zoos compared to in the wild, such as visitors and lack of environmental stimulation. This study included two projects conducted on the drills at Parken Zoo in Eskilstuna where I investigated: 1) the effect of visual barriers on the behaviour of the drills and if the visual barriers can moderate the visitor effect on the drills and 2) how outdoor-only access together with feeding enrichment (frozen fruit and tube feeders) affects the behaviour of the drills. 1/0- sampling method was used when observing the behaviours of the drills with 1 minute-intervals. Resting/Sleeping increased, while social agonistic behaviour and stereotypies decreased with visual barriers. A moderated visitor effect was shown in resting/sleeping and social affiliative behaviour in the drills with visual barriers. However, social agonistic behaviour and visitor interaction were still affected by visitors after the installation of the visual barriers, implying that the drills still find visitors stressful to some extent and that further alterations on the observation area viewing the indoor enclosure is recommended for the welfare of the drills. With outdoor-only access together with feeding enrichment, locomotion, foraging/eating and body-shaking increased, while resting/sleeping, social affiliative and agonistic behaviour, stereotypies, visitor interaction, scratching and self-grooming decreased. This suggests that outdoor-only access and feeding enrichment improve the behaviour of the drills and would be a valid option during summer season for the drills at Parken Zoo.
Genetic variation in transpiration efficiency and relationships between whole plant and leaf gas exchange measurements in Saccharum spp. and related germplasm

Fifty-one genotypes of sugarcane (Saccharum spp.) or closely related germplasm were evaluated in a pot experiment to examine genetic variation in transpiration efficiency. Significant variation in whole plant transpiration efficiency was observed, with the difference between lowest and highest genotypes being about 40% of the mean. Leaf gas exchange measurements were made across a wide range of conditions. There was significant genetic variation in intrinsic transpiration efficiency at a leaf level as measured by leaf internal CO2 (Ci) levels. Significant genetic variation in Ci was also observed within subsets of data representing narrow ranges of stomatal conductance. Ci had a low broad sense heritability (Hb = 0.11) on the basis of single measurements made at particular dates, because of high error variation and genotype × date interaction, but broad sense heritability for mean Ci across all dates was high (Hb = 0.81) because of the large number of measurements taken at different dates. Ci levels among genotypes at mid-range levels of conductance had a strong genetic correlation (−0.92 ± 0.30) with whole plant transpiration efficiency but genetic correlations between Ci and whole plant transpiration efficiency were weaker or not significant at higher and lower levels of conductance. Reduced Ci levels at any given level of conductance may result in improved yields in water-limited environments without trade-offs in rates of water use and growth. Targeted selection and improvement of lowered Ci per unit conductance via breeding may provide longer-term benefits for water-limited environments but the challenge will be to identify a low-cost screening methodology.
Return-Oriented Rootkits: Bypassing Kernel Code Integrity Protection Mechanisms

Protecting the kernel of an operating system against attacks, especially injection of malicious code, is an important factor for implementing secure operating systems. Several kernel integrity protection mechanism were proposed recently that all have a particular shortcoming: They cannot protect against attacks in which the attacker re-uses existing code within the kernel to perform malicious computations. In this paper, we present the design and implementation of a system that fully automates the process of constructing instruction sequences that can be used by an attacker for malicious computations. We evaluate the system on different commodity operating systems and show the portability and universality of our approach. Finally, we describe the implementation of a practical attack that can bypass existing kernel integrity protection mechanisms.
The development and uses of EPA’s SPECIATE database

SPECIATE is the U.S. Environmental Protection Agency’s (EPA) repository of volatile organic compounds (VOCs) and particulate matter (PM) speciation profiles of air pollution sources. These source profiles can be used to (1) provide input to chemical mass balance (CMB) receptor models; (2) verify profiles derived from ambient measurements by multivariate receptor models (e.g., factor analysis and positive matrix factorization); (3) interpret ambient measurement data; and (4) create speciated emission inventories for regional haze, climate, and photochemical air quality modeling. This paper describes the SPECIATE v4.2 database, provides specific examples of its use, and makes recommendations for future improvements.
The Impact of Body Mass Index and Weight Changes on Disability Transitions and Mortality in Brazilian Older Adults

The aim of this study was to examine the association between body mass index and weight changes on disability transitions and mortality among Brazilian older adults. Longitudinal data from the Health, Well-Being, and Aging in Latin America and the Caribbean Study conducted in São Paulo, Brazil (2000 and 2006), were used to examine the impact of obesity on disability and mortality and of weight changes on health transitions related to disability. Logistic and multinomial regression models were used in the analyses. Individuals who were obese were more likely than those of normal weight to have limitations on activities of daily living (ADL), instrumental activity of daily living (IADL), and Nagi's limitations. Obesity was associated with higher incidence of ADL and IADL limitations and with lower recovery from Nagi's limitations. Compared to those who maintained their weight, those who gained weight experienced higher incidence of ADL and Nagi's limitations, even after controlling for initial body mass index. Higher mortality among overweight individuals was only found when the reference category was “remaining free of Nagi limitations. ” The findings of the study underline the importance of maintaining normal weight for preventing disability at older ages.
The effect of device geometry on the static and dynamic response of carbon nanotube field effect transistors

A numerical study of ohmic contact carbon nanotube field effect transistors is presented. The effect of the gate-source and gate-drain spacers on the static and dynamic response of the device was studied. Simulation results suggest that by appropriately selecting the gate-source and gate-drain spacers both the dynamic and static characteristics of the device are improved.
Metabolic Syndrome and Cognitive Disorders: Is the Sum Greater Than Its Parts?

Given the anticipated exponential increase in both the incidence and prevalence of dementia, it is critical to identify preventative strategies and improved treatments for this disorder. The metabolic syndrome is comprised of 5 cardiovascular risk factors that include abdominal obesity, hypertriglyceridemia, low high-density lipoprotein levels, hypertension, and hyperglycemia. The prevalence of the metabolic syndrome, similar to that for cognitive disorders, increases dramatically with age. Several possible mechanisms may explain an association between the metabolic syndrome and cognitive decline including microvascular and macrovascular disease, inflammation, adiposity, and insulin resistance. Although some of the individual components of the metabolic syndrome have been linked to risk of developing dementia and cognitive impairment, few studies have looked at the components of the metabolic syndrome as a whole. We found, in 3 separate studies involving elders of different ethnicities, that the metabolic syndrome is a risk factor for accelerated cognitive aging. This was especially true for elders with the metabolic syndrome and with elevated serum level of inflammation. If metabolic syndrome is associated with increased risk of developing cognitive impairment, regardless of mechanism, then early identification and treatment of these individuals might offer avenues for disease course modification.
[Correlation between risk factors of hearing lose and results of initial hearing screening in 1021 neonates].

OBJECTIVE To explore the risk factors of the newborns who failed initial hearing screening by analysing the distortion production otoacoustic emission (DPOAE) results of 1021 newborns with potential risk factors of hearing loss. METHOD All newborns, who were born in obstetrical department and admitted in the neonatal department of the Nanfang Hospital during June 2009 to January 2012 and underwent initial hearing screening, were included in this study. Their clinical data and DPOAE results were analyzed retrospectively in order to identify the risk factors for failure of initial hearing screening in infants; cases who failed the DPOAE test were followed up by telephone interviews. RESULT (1) One hundred and thirty-seven cases (13.42%) of the 1021 newborns did not pass the hearing screening. 51 cases (5.00%) did not pass the test in both ears. Meanwhile, left ear in 47 cases (4.60%) and right ear in another 39 cases (3.82%) failed the test respectively. (2) Univariate analysis showed that 14 factors had significant influence on the hearing screening results, such as birth weight, small for gestational age, multiple pregnancy, gestational age, delivery mode, oligohydramnion, oxytocin, blood sugar level of newborn, Apgar scores at 1 min, exposed prenatally to glucocorticoid, maxillofacial deformity, hypoxic-ischemic encephalopathy, neonatal respiratory distress syndrome and neonatal asphyxia (P < 0.01). (3) Multivariate Logistic regression analysis suggested that birthweight less than 1500 g, multiple pregnancy, Apgar scores of 0-4 at 1 min, exposed prenatally to glucocorticoid and maxillofacial deformity were risk factors for failure of initial hearing screening (OR were 3.132, 1.808, 2.615, 1.827 and 12.174 respectively; 95% CI were 1.466-6.691, 1.120-2.917, 1.317-5.336, 1.130-2.953 and 1.986-74.632 respectively). (4) Results of telephone interviews revealed that Apgar scores of 0-4 at 1 min would be a risk factor of language development. CONCLUSION Birthweight less than 1500 g, multiple pregnancy, Apgar scores of 0-4 at 1 min, exposed prenatally to glucocorticoid and maxillofacial deformity are risk factors of failure of initial hearing screening among newborns with potential hearing loss. Monitoring of the hearing condition of the infants at risk should be strengthened.
Institutional Corruption and Election Fraud: Evidence from a Field Experiment in Afghanistan†

We investigate the relationship between political networks, weak institutions, and election fraud during the 2010 parliamentary election in Afghanistan combining: (i) data on political connections between candidates and election officials; (ii) a nationwide controlled evaluation of a novel monitoring technology; and (iii) direct measurements of aggregation fraud. We find considerable evidence of aggregation fraud in favor of connected candidates and that the announcement of a new monitoring technology reduced theft of election materials by about 60 percent and vote counts for connected candidates by about 25 percent. The results have implications for electoral competition and are potentially actionable for policymakers. (JEL C93, D02, D72, K42, O17)
ERP implementation through critical success factors' management

Purpose – The purpose of this paper is to identify practical activities that are essential for managing enterprise resource planning (ERP) implementation projects and that answer to the expectations of the widely recognized critical success factors (CSFs). Design/methodology/approach – This work is based on an extensive literature review on CSF, which has been followed by a Delphi survey with a panel of ERP experts. For each CSF, it obtained a range, validated by experts, of practical actions to perform, supported by the resolution of the problems usually encountered in these areas.Findings – The work carried out has a practical scope: the principles of the proposed method directly affect all actors in ERP projects and gives them practical results that they can apply immediately. When applied in the framework of the methodology the paper suggests, these actions will result in better oversight over the requirements of each area of expertise. In this way, overall grasp of the project is facilitated, reducing.
An estimation model for footstep modifications of biped robots

Pushing, soft ground contact and other unknown large disturbances can cause humanoid robots to fall. In order to face such problems, an accurate and fast model of the robot is necessary to estimate the state at a certain time in the future using only current measurements. We approximate the robot by a three-mass model with two degrees of freedom. Unilateral compliant contacts and a closed-loop control similar to the one used on the real robot are included additionally. Utilizing this model it is possible to predict the robot's behavior and calculate compensating motions for different disturbance cases. Furthermore, it is possible to integrate the estimation results into the real-time control system of our biped LOLA. Simulation and experimental results demonstrate the effectiveness and the advantages of the proposed method.
Automated Quantification of DNA Aneuploidy by Image Cytometry as an Adjunct for the Cytologic Diagnosis of Malignant Effusion

DNA aneuploidy is a cancer biomarker, which may have a potential diagnostic value in body effusion specimen. DNA aneuploidy is determined by measuring the DNA content of tested cells and comparing them with diploid cells (2c). In order to assess the value of automated DNA image cytometry (DNA-ICM) in the cytologic diagnosis of effusion, we measured DNA ploidy using an automated DNA-ICM analysis system in 126 consecutive effusion specimens and followed the cases for histologic diagnosis. Half of each effusion specimen was used to prepare cytologic smears for conventional cytologic diagnosis, while the other half was used to prepare a monolayer slide stained by Feulgen stain for automated ICM. By using Youden index, we found that 4 cells exceeding 2.5c is the optimal cut off value for aneuploidy, which has a sensitivity of 88.3% and specificity of 100% for diagnosis of malignant effusion. We also found that the DNA aneuploidy thresholds used for other types of cytologic specimens cannot be used in the diagnosis of effusion specimens. Our study demonstrated that automated DNA image cytometry is a simple, practical and cost-effective method for adjunct diagnosis of malignant effusion.