Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Distribution of Noncapsular Meningococcal Group B Vaccine Antigens in Neisseria lactamica

ABSTRACT The poor immunogenicity of the meningococcal serogroup B (MenB) capsule has led to the development of vaccines targeting subcapsular antigens, in particular the immunodominant and diverse outer membrane porin, PorA. These vaccines are largely strain specific; however, they offer limited protection against the diverse MenB-associated diseases observed in many industrialized nations. To broaden the scope of its protection, the multicomponent vaccine (4CMenB) incorporates a PorA-containing outer membrane vesicle (OMV) alongside relatively conserved recombinant protein components, including factor H-binding protein (fHbp), Neisseria adhesin A (NadA), and neisserial heparin-binding antigen (NHBA). The expression of PorA is unique to meningococci (Neisseria meningitidis); however, many subcapsular antigens are shared with nonpathogenic members of the genus Neisseria that also inhabit the nasopharynx. These organisms may elicit cross-protective immunity against meningococci and/or occupy a niche that might otherwise accommodate pathogens. The potential for 4CMenB responses to impact such species (and vice versa) was investigated by determining the genetic distribution of the primary 4CMenB antigens among diverse members of the common childhood commensal, Neisseria lactamica. All the isolates possessed nhba but were devoid of fhbp and nadA. The nhba alleles were mainly distinct from but closely related to those observed among a representative panel of invasive MenB isolates from the same broad geographic region. We made similar findings for the immunogenic typing antigen, FetA, which constitutes a major part of the 4CMenB OMV. Thus, 4CMenB vaccine responses may impact or be impacted by nasopharyngeal carriage of commensal neisseriae. This highlights an area for further research and surveillance should the vaccine be routinely implemented.
Pessimism in the stochastic analysis of real-time systems: concept and applications

The exact stochastic analysis of most real-time systems is becoming unaffordable in current practice. On one side, the exact calculation of the response time distribution of the tasks is not possible except for simple periodic and independent task sets. On the other side, in practice, tasks introduce complexities like release jitter, blocking in shared resources, stochastic dependencies, etc, which can not be handled by the periodic and independent task set model. This paper introduces the concept of pessimism in the stochastic analysis of real-time systems in the following sense: the exact probability of missing any deadline is always lower than that derived from the pessimistic analysis. Therefore, if real-time constraints are expressed as probabilities of missing deadlines, the pessimistic stochastic analysis provides safe results. Some applications of the pessimism concept are presented. Firstly, the practical problems that arise in the stochastic analysis of periodic and independent task sets are addressed. Secondly, we extend to the stochastic case some well known techniques of the deterministic analysis, such as the blocking in shared resources, and the task priority assignment.
Neuronal activity in monkey ventral striatum related to the expectation of reward

Projections from cortical and subcortical limbic structures to the basal ganglia are predominantly directed to the ventral striatum. The present study investigated how the expectation of external events with behavioral significance is reflected in the activity of ventral striatal neurons. A total of 420 neurons were studied in macaque monkeys performing in a delayed go-no-go task. Lights of different colors instructed the animal to do an arm-reaching movement or refrain from moving, respectively, when a trigger light was illuminated a few seconds later. Task performance was reinforced by liquid reward in both situations. A total of 60 ventral striatal neurons showed sustained increases of activity before the occurrence of individual task events. In 43 of these neurons, activations specifically preceded the delivery of reward, independent of the movement or no-movement reaction. In a series of additional tests, these activations were time locked to the subsequent reward, disappeared within a few trials when reward was omitted, and were temporally unrelated to mouth movements. Changes in the appetitive value of the reward liquid modified the magnitude of activations, suggesting a possible relationship to the hedonic properties of the expected event. Activations also occurred when reward was delivered in a predictable manner outside of any behavioral task. These data suggest that neurons in the ventral striatum are activated during states of expectation of individual environmental events that are predictable to the subject through its past experience. The prevalence of activations related to the expectation of reward suggests that ventral striatal neurons have access to central representations of reward and thereby participate in the processing of information underlying the motivational control of goal-directed behavior.
Comparison between somatostatin analogues and ACE inhibitor in the NOD mouse model of diabetic kidney disease.

BACKGROUND The growth hormone (GH)-insulin-like growth factor (IGF)-SST (SST) axis is involved in diabetic nephropathy (DN). We have recently shown a beneficial effect on diabetic kidney disease markers by the use of a novel somatostatin (SST) analogue (PTR-3173) (S). The purpose of this study is to compare the effects of S with a previously used SST analogue (octreotide) and an ACE inhibitor (ACEi), a standard of care in DN. METHODS Non-obese diabetic mice (a model of type I diabetes) were treated with either S (DS), octreotide (DO), enalapril (DA), or PTR-3173 and enalapril (DAS group) for 3 weeks. RESULTS Diabetic renal hypertrophy was blunted in the DS and DO groups only. Serum GH and IGF-I were markedly increased and decreased, respectively, in the D group, a change significantly blunted in DO and DS. Diabetic hyperfitration and albuminuria were blunted in all the four treated diabetic groups. The marked deposition of type IV collagen and PAS material were mildly decreased in DA, but more markedly reduced in DS as well as DO. Diabetic renal laminin accumulation was suppressed in all treated animal groups. No synergistic effect was observed for any parameter in the combination group DAS. CONCLUSION SST analogues exert beneficial effects in most parameters of diabetic kidney disease to the same extent as the ACEi. Enalapril treatment had no effect on renal hypertrophy and did not cause a significant decrease in mesangial type IV collagen deposition. A synergistic effect of combined SST-ACEi therapy could not be shown in this study.
Reducing the space complexity of a Bayes coding algorithm using an expanded context tree

The context tree models are widely used in a lot of research fields. Patricia[7] like trees are applied to the context trees that are expanded according to the increase of the length of a source sequence in the previous researches of non-predictive source coding and model selection. The space complexity of the Patricia like context trees are O(t) where t is the length of a source sequence. On the other hand, the predictive Bayes source coding algorithm cannot use a Patricia like context tree, because it is difficult to hold and update the posterior probability parameters on a Patricia like tree. So the space complexity of the expanded trees in the predictive Bayes coding algorithm is O(t2). In this paper, we propose an efficient predictive Bayes coding algorithm using a new representation of the posterior probability parameters and the compact context tree holding the parameters whose space complexity is O(t).
TTP/A: A Low-Cost, Highly Efficient, Time-Triggered Fieldbus Architecture

TTP/A is the fieldbus protocol of the Time Triggered Architecture (TTA). It provides periodic transmission of realtime data and allows for on-line configuration, diagnostics, and maintenance by use of an interface file system. It is well integrated with the TTP/C protocol and is designed to meet the requirements of a low-cost sensor/actuator bus. TTP/A is a master-slave protocol where the master establishes a common time base within a TTP/A cluster. Since the master establishes the time base prior to the communication of slaves, the protocol can be implemented with low-cost on-chip RC oscillators for the slaves. Using a standard UART-based serial interface as physical layer, the slave TTP/A protocol can be implemented in very low cost Commercial Off-The-Shelf (COTS) hardware.
Changing minds: Bounded rationality and heuristic processes in exercise-related judgments and choices.

Theories currently used to understand, predict, and promote physical activity and exercise represent information-processing models of the mind. A fundamental assumption underpinning these theories is that human judgment and decision-making processes are rational. Thus, interventions derived from these models are aimed to enhance “data input” (e.g., provide complete, accurate, and compelling information about health benefits) with the expectation that the rational evaluation of these data will result in the desired behavioral “output. ” Given the modest effectiveness of interventions based on these models, we designed 2 experiments testing the validity of the assumption of rationality, focusing specifically on exercise-related judgments and decisions. In Experiment 1, exercise judgments were altered by shifting an arbitrary anchor, whose presence should have had no bearing on these judgments. In Experiment 2, the preference between a target exercise session and an alternative was increased by the mere addition of a third “decoy” exercise option. Together, these experiments demonstrate that important motivational variables, including the perceived desirability of exercise, affective attitude, intention, affective forecasts, and exercise choices can be manipulated in a predictable direction without providing any new relevant information, but by merely targeting specific, well-characterized heuristics. Therefore, these data provide evidence that the “bounded” nature of human rationality also manifests itself in exercise judgments and decisions. Researchers and exercise practitioners should consider incorporating heuristic processes within dual-process theoretical models of physical activity and exercise behavior.
Systematic Evaluation of Drosophila CRISPR Tools Reveals Safe and Robust Alternatives to Autonomous Gene Drives in Basic Research

The Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR associated (CRISPR/Cas) technology allows rapid, site-specific genome modification in a wide variety of organisms . Proof-of-principle studies in Drosophila melanogaster have used various CRISPR/Cas tools and experimental designs, leading to significant uncertainty in the community about how to put this technology into practice. Moreover, it is unclear what proportion of genomic target sites can be modified with high efficiency. Here, we address these issues by systematically evaluating available CRISPR/Cas reagents and methods in Drosophila. Our findings allow evidence-based choices of Cas9 sources and strategies for generating knock-in alleles. We perform gene editing at a large number of target sites using a highly active Cas9 line and a collection of transgenic gRNA strains. The vast majority of target sites can be mutated with remarkable efficiency using these tools. We contrast our method to recently developed autonomous gene drive technology for somatic and germline genome engineering and conclude that optimized CRISPR with independent transgenes is as efficient, more versatile, and does not represent a biosafety risk.
Web-crawling reliability

In this article, I investigate the reliability, in the social science sense, of collecting informetric data about the World Wide Web by Web crawling. The investigation includes a critical examination of the practice of Web crawling and contrasts the results of content crawling with the results of link crawling. It is shown that Web crawling by search engines is intentionally biased and selective. I also report the results of a large-scale experimental simulation of Web crawling that illustrates the effects of different crawling policies on data collection. It is concluded that the reliability of Web crawling as a data collection technique is improved by fuller reporting of relevant crawling policies.
Racialized classroom practices in a diverse Amsterdam primary school: the silencing, disparagement, and discipline of students of color

Abstract In both Europe and the US, racial and ethnic minority students experience discrimination at the hands of teachers that negatively impacts academic achievement. In the US, scholars have documented how a predominantly white teaching force racializes students of color through discipline and low expectations, which impact educational attainment. But in Europe, the denial of race’s existence hinders research regarding structural explanations for minority educational inequality and often explains low educational attainment as a function of cultural differences. Examining classroom practices in a diverse Amsterdam primary school, this article documents racializing mechanisms that found minority students disproportionately disparaged, disciplined, and silenced. In addition, many were students under-recommended to higher level secondary school tracks. These findings reveal that Dutch schools are not racially meritocratic institutions and are relevant for scholars in the Netherlands and all other nations with educational institutions dominated by colorblind ideologies, white norms, and large immigrant populations.
Analysis of non-HLA genomic risk factors in HLA-matched unrelated donor hematopoietic cell transplantation for chronic myeloid leukemia

Background Allogeneic hematopoietic cell transplantation is the main curative therapy for patients with chronic myeloid leukemia who do not respond to tyrosine kinase inhibitors. It has been proposed that non-human leukocyte antigen gene polymorphisms influence outcome after hematopoietic cell transplantation and could be used alongside traditional patient-donor and transplant characteristics to create a recipient risk profile associated with allogeneic hematopoietic cell transplantation. Design and Methods A previous study from the European Group for Blood and Marrow Transplantation showed that the absence of recipient tumor necrosis factor receptor II, absence of donor interleukin 10 ATA/ACC and presence of donor interleukin 1 receptor antagonist allele 2 genotypes were associated with decreased survival and increased non-relapse mortality in adult patients with chronic myeloid leukemia undergoing myeloablative human leukocyte antigen-identical sibling transplantation. To explore these associations in unrelated donor transplantation, these polymorphisms were genotyped in 383 adult patients with chronic myeloid leukemia who underwent hematopoietic cell transplantation from unrelated donors matched for 10/10 human leukocyte antigens. Results The polymorphisms were not associated with overall survival, non-relapse mortality, relapse or acute graft-versus-host disease in the unrelated donor cohort. Comparison of the unrelated donor and human leukocyte antigen-identical sibling cohorts showed differences in survival and clinical characteristics. Conclusions We did not confirm that non-human leukocyte antigen polymorphisms were associated with outcomes in myeloablative unrelated donor hematopoietic cell transplantation for chronic myeloid leukemia, possibly because of the strong association between clinical variables and outcome which masked more subtle genetic effects.
Antigen-Experienced CD4lo T Cells Are Linked to Deficient Contraction of the Immune Response in Autoimmune Diabetes

Following proper activation, naïve “CD4lo” T cells differentiate into effector T cells with enhanced expression of CD4 -“CD4hi” effectors. Autoimmune diabetes-prone NOD mice display a unique set of antigen-experienced “CD4lo” T cells that persist after primary stimulation. Here, we report that a population of such cells remained after secondary and tertiary TCR stimulation and produced cytokines upon antigenic challenge. However, when NOD blasts were induced in the presence of rIL-15, the number of antigen-experienced “CD4lo” T cells was significantly reduced. Clonal contraction, mediated in part by CD95-dependent activation-induced cell death (AICD), normally regulates the accumulation of “CD4hi” effectors. Interestingly, CD95 expression was dramatically reduced on the AICD-resistant NOD “CD4lo” T cells. Thus, while autoimmune disease has often been attributed to the engagement of robust autoimmunity, we suggest that the inability to effectively contract the immune response distinguishes benign autoimmunity from progressive autoimmune diseases that are characterized by chronic T cell-mediated inflammation.
Transmigration of Mandibular Canines

The purpose of this paper is to present the first case of unusual reverse oblique (110 degrees to midsagittal plane) migration of mandibular right canine crossing the jaw midline and piercing the lower border of the mandible at the level of the opposite canine and also to report two more cases of transmigrated mandibular canine and one case of transmigrating mandibular canine. Mandibular canines are “cornerstone” of dental arch; their importance is manifested by their efficiency in masticatory function, stability of dental arch, and aid in maintaining natural facial expression. Early detection of this anomaly can help preserving these canines by orthodontic intervention or by surgical transplantation. This developmental anomaly is properly diagnosed by radiographic evaluation, which is primarily based on the panoramic radiograph. In patients with overretained deciduous canines or missing permanent canines, an intraoral radiograph should be supplemented with panoramic radiograph. This paper discusses the importance of early diagnosis of canine transmigration in treatment planning and reviews the various possible treatment options.
Connectivity of Default-Mode Network Is Associated with Cerebral Edema in Hepatic Encephalopathy

Cerebral edema, a well-known feature of acute liver disease, can occur in cirrhotic patients regardless of hepatic encephalopathy (HE) and adversely affect prognosis. This study characterized and correlated functional HE abnormalities in the brain to cerebral edema using resting-state functional magnetic resonance imaging (rs-fMRI) and diffusion tensor imaging (DTI). Forty-one cirrhotic patients (16 without HE, 14 minimal HE, 11 overt HE) and 32 healthy controls were assessed. The HE grade in cirrhotic patients was evaluated by the West Haven criteria and neuro-psychological examinations. Functional connectivity correlation coefficient (fc-CC) of the default mode network (DMN) was determined by rs-fMRI, while the corresponding mean diffusivity (MD) was obtained from DTI. Correlations among inter-cortical fc-CC, DTI indices, Cognitive Ability Screening Instrument scores, and laboratory tests were also analyzed. Results showed that gradual reductions of HE-related consciousness levels, from “without HE” or “minimal HE” to “overt HE”, correlated with decreased anterior-posterior fc-CC in DMN [F(4.415), p = 0.000)]. The MD values from regions with anterior-posterior fc-CC differences in DMN revealed significant differences between the overt HE group and other groups. Increased MD in this network was inversely associated with decreased fc-CC in DMN and linearly correlated with poor cognitive performance. In conclusion, cerebral edema can be linked to altered cerebral temporal architecture that modifies both within- and between-network connectivity in HE. Reduced fc-CC in DMN is associated with behavior and consciousness deterioration. Through appropriate targets, rs-fMRI technology may provide relevant supplemental information for monitoring HE and serve as a new biomarker for clinical diagnosis.
The face‐inversion effect can be explained by the capacity limitations of an orientation normalization mechanism

The effect of orientation on face recognition was explored by selectively altering facial components (eyes and mouth) or by changing configural information (distances between components). Regardless of the type of change, a linear increase in reaction time for same-different judgments was revealed when the faces were rotated away from upright. The analyses of error scores indicated that the detection of altered components was only slightly affected by orientation, while orientation had a detrimental effect on the detection of configural changes. These results are consistent with the assumption that rotated faces overtax an orientation normalization mechanism so that they have to be processed by mentally rotating parts, which makes it difficult to recover configural information.
Cognitive Vulnerability to Mood Disturbance in an Exercise Withdrawal Paradigm

Depressive symptoms are more common among sedentary individuals with longitudinal studies supporting inactivity as a potential risk factor for mood disturbances. Observational and experimental designs find that lack of exercise or exercise deprivation is associated with increased depressive and anxiety symptoms, fatigue, and pain. However, literature has not examined risk factors influencing mood deterioration in response to exercise deprivation. The current study tested the hypothesis that physically active individuals with high levels of cognitive vulnerability (i.e., a tendency towards negative thought content and processes when under stress) are at high risk for mood disturbance when undergoing exercise cessation. Community adults who met guidelines for recommended physical activity (N=36) were examined in a 4-week prospective, longitudinal study. Mood was assessed with the Beck Depression Inventory-Second Edition, the Beck Anxiety Inventory, and the Brief Profile of Mood States at baseline, after two weeks of maintained exercise, and after one and two weeks of exercise cessation. Cognitive vulnerability variables (i.e., dysfunctional attitudes, brooding rumination, cognitive reactivity) were assessed following the maintained exercise phase. Similar to prior studies, results indicated a main effect of time, such that depressive and anxiety symptoms increased over the exercise cessation protocol. Results additionally lend support for a vulnerability-stress model, with brooding rumination identified as a risk factor for the development of symptoms during exercise deprivation. This study suggests that individuals who engage in brooding rumination to cope with negative affect are at elevated risk for mood symptoms when ceasing their exercise routine.
DAHC-tree: An Effective Index for Approximate Search in High-Dimensional Metric Spaces

Similarity search in high-dimensional metric spaces is a key operation in many applications, such as multimedia databases, image retrieval, object recognition, and others. The high dimensionality of the data requires special index structures to facilitate the search. A problem regarding the creation of suitable index structures for high-dimensional data is the relationship between the geometry of the data and the organization of an index structure. In this paper, we study the performance of a new index structure, called Divisive-Agglomerative Hierarchical Clustering tree (DAHC-tree), which reduces the effects imposed by the above liability. DAHC-tree is constructed by dividing and grouping the data set into compact clusters. We perform a rigorous experimental design and analyze the trade-offs involved in building such an index structure. Additionally, we present extensive experiments comparing our method against state-of-the-art of exact and approximate solutions. The conducted analysis and the reported comparative test results demonstrate that our technique significantly improves the performance of similarity queries.