Miracle-dz/UniFAR-FTUs huggingface dataset:
Lessons learned from the psychosis high-risk state: towards a general staging model of prodromal intervention

Background The past two decades have seen exponential clinical and research interest in help-seeking individuals presenting with potentially prodromal symptoms for psychosis. However, the epidemiological validity of this paradigm has been neglected, limiting future advancements in the field. Method We undertook a critical review of core epidemiological issues underlying the clinical high-risk (HR) state for psychosis and which model of prodromal intervention is best suited for mental health. Results The HR state for psychosis model needs refining, to bring together population-based findings of high levels of psychotic experiences (PEs) and clinical expression of risk. Traditionally, outcome has been attributed to ‘HR criteria’ alone rather than taking into account sampling strategies. Furthermore, the exclusive focus on variably defined ‘transition’ obscures true variation in the slow and non-linear progression across stages of psychopathology. Finally, the outcome from HR states is variable, indicating that the underlying paradigm of ‘schizophrenia light progressing to schizophrenia’ is inadequate. Conclusions In the general population, mixed and non-specific expression of psychosis, depression, anxiety and subthreshold mania is common and mostly transitory. When combined with distress, it may be considered as the first, diagnostically neutral stage of potentially more severe psychopathology, which only later may acquire a degree of diagnostic specificity and possible relative resistance to treatment. Therefore, rather than creating silos of per-disorder ultra-HR syndromes, an early intervention focus on the broad syndrome of early mental distress, requiring phase-specific interventions, may be more profitable.
Foodborne Sources of Bacteria Associated With Human Obesity

Foodborne Sources of Bacteria Associated with Human Obesity (April 2008) Katherine Grace McElhany Department of Biology Texas A&M University Research Advisor: Dr. Suresh Pillai Department of Poultry Science & Nutrition and Food Science Recently published research has suggested that the microbial ecology of the digestive system may play a role in obesity. Obese people have been shown to have a higher proportion of bacteria from the Firmicutes division and a lower proportion of bacteria from the Bacteroidetes division in their gut. The goal of this study was to characterize the microbial communities in specific foods using a combination of microbiology and metagenomic techniques. The ultimate goal of this project was to identify specific foods that may be introducing the Firmicutes and Bacteroidetes bacterial groups into the human gut. Nine commonly consumed foods, both natural and processed, were selected for this study and were purchased from a retail outlet in College Station, TX. These included wheat bread, whole milk, spinach, low-fat yogurt, medium cheddar cheese, 80/20 ground beef, salmon, banana, and skinless chicken breast samples. The food samples were plated on Tryptic Soy Agar (TSA) media to determine the aerobic and anaerobic bacterial loads and to isolate bacteria. The total microbial community was extracted from these food samples and the 16S rRNA gene sequences of the microbiome
Double Unilimb Z-Plastic Repair of Microform Cleft Lip

Background: Microform unilateral cleft lip is characterized by 1) notched mucosal margin; 2) thin medial vermilion; 3) elevated medial peak of Cupid's bow; 4) furrowed philtral column; 5) hypoplastic orbicularis oris; and 6) minor nasal deformity. Methods: The author's registry of unilateral incomplete cleft lip was culled for patients with microform cleft lip. Operative correction included: double-limb Z-plasty at the vermilion-cutaneous and vermilion-mucosal junctions; eversion of orbicularis oris; augmentation of philtral ridge with a dermal graft; medial positioning of the alar base; and elevation of the lower lateral cartilage. Results: Microform phenotype was found in 33 of 360 infants (9.2 percent) with unilateral incomplete cleft lip. Male-to-female and left-to-right ratio were both 2:1. Median age at presentation was 11 months (range, 2 weeks to 9 years). Twenty-three patients had a double unilimb Z-plastic repair (including dermal graft and nasal correction). No revisions have been necessary at median follow-up of 5 years, however, 13 percent of children lacked prominence of the upper philtral column and one-third of children exhibited minor nostril asymmetry. Conclusions: Double unilimb Z-plasty corrects the vertical asymmetry in a microform cleft lip while limiting the scar to the lower one-half of the lip. The philtral ridge is formed by repair of the muscular diastasis and onlay of a dermal graft. Components of this technique are applicable to secondary cleft deformities, such as elevated peak of the Cupid's bow and inadequate philtral ridge.
Neuron‐specific RNA interference using lentiviral vectors

Viral vectors have been used in several different settings for the delivery of small hairpin (sh) RNAs. However, most vectors have utilized ubiquitously‐expressing polymerase (pol) III promoters to drive expression of the hairpin as a result of the strict requirement for precise transcriptional initiation and termination. Recently, pol II promoters have been used to construct vectors for RNA interference (RNAi). By embedding the shRNA into a micro RNA‐context (miRNA) the endogenous miRNA processing machinery is exploited to achieve the mature synthetic miRNA (smiRNA), thereby expanding the possible promoter choices and eventually allowing cell type specific down‐regulation of target genes.
Genomic and clinical data correlation for relapse prediction in cancer samples

This chapter aims to describe concepts and methods required to understand the development of this investigation. An introduction to cancer research and bioinformatics is provided, considering a description, brief historical review, current status and important challenges for the future. The chapter also considers techniques in statistics and data analysis that provide the basis for the search of relations between genomic and clinical data; this includes data dimensionality reduction techniques, clustering and regression, gene ontology, pathway and co-regulation analysis and the analysis of gene expression distribution. For each subject, a definition is provided, along with a short explanation on how to implement it. Since the beginning of the study of systems biology as an interdisciplinary subject, many concepts have been applied and redeveloped to provide innovative views to old biology problems. With the explosion of data collection, the analysis has become more important, and is still one step behind, since all the collected data remains a partial mystery. The methodologies and possibilities of data analysis are too numerous to be explained in total; however this chapter comprises many of the basic techniques in bioinformatics, and explains the ones that we have used in this investigation.
Mathematisches Forschungsinstitut Oberwolfach Report No . 13 / 2004 Discrepancy Theory and Its Applications

Balanced partitions of vector sequences Imre Bárány Let d, N ∈ N. Let ‖ · ‖ be any norm on R and B = {v ∈ R : ‖v‖ ≤ 1} its unit ball. Some time ago I proved the following result [2]: Let v1, v2, . , vN ⊆ B be a finite sequence of vectors. Then there are signs εi ∈ {−1, 1} such that ∥∥∥∥∥ ∑ i∈[n] εivi ∥∥∥∥∥ ≤ 2d for all n ∈ [N ] = {1, 2, . , N}. In other words, there is a partition [N ] = I1 ∪ I2 such that ∥∥∥∥∥ ∑ i∈Ij∩[n] vi − 1 2 ∑ i∈[n] vi ∥∥∥∥∥ ≤ d for all n ∈ [N ] and j ∈ [2]. This partitioning version of the theorem was extended to partitions into r > 2 classes with error bound (r − 1)d in [3]. In my talk, I explained how the factor (r − 1) can be replaced by a constant. To state this result precisely, we introduce some convenient notation: Let V be the given sequence of vectors v1, v2, . , vN . We use the (non-standard) notation ∑
Shaping physical machine topology in distributed data center networks

Physical machines (PMs) constitute the hardware infrastructure in data centers. Proper distribution and placement of PMs plays an important role in determining the system performance. Existing PM placement approaches generally ignore the demands of virtual machines (VMs), resulting in a poor resource utilization and service QoS. In this paper, we focus on the PM placement problem in a given optical network (called the optical layer) with given traffic demands on the VM-layer. By jointly considering optical and VM layers, we formulate an ILP (Integer Linear Program) to shape the PM-layer topology, while minimizing the overall cost of PM placement and VM mapping. To combine delay and transmission costs on each optical link, we define a cost factor θ, which can be used to adjust the impact of service delay. Extensive numerical simulations are carried out to validate the correctness of our ILP and the flexibility of our scheme.
Predictive value of remnant-like particle cholesterol as an indicator of coronary artery stenosis in patients with normal serum triglyceride levels.

OBJECTIVE We designed the present study to evaluate the association of various lipid and fibrinolytic components with coronary artery stenosis with respect to the triglyceride (TG) level. METHODS Levels of TG, remnant-like particle cholesterol (RLP-C), total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), lipoprotein-(a), uric acid, blood glucose, tissue plasminogen activator (t-PA), t-PA inhibitor type 1, antithrombin III, and protein C were measured in 208 patients who underwent diagnostic coronary angiograms. PATIENTS Of these 208 patients, 59 were hypertriglyceridemic (150 mg/dl or higher) and 149 were normotriglyceridemic. RESULTS Both LDL-C and HDL-C showed significant differences between patients with and those without coronary artery stenosis in both hypertriglyceridemic and normotriglyceridemic patient subgroups. However, RLP-C showed a significant difference in the normotriglyceridemic patient subgroup (p=0.012) but not in the hypertriglyceridemic patient subgroup (p=0.736). CONCLUSION Our current retrospective study disclosed that RLP-C levels are closely associated with coronary artery stenosis in patients with normal TG levels.
Diffuse large B-cell non-Hodgkin's lymphoma: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.

Diagnosis should be made on the basis of a surgical specimen/ excisional lymph node or extranodal tissue biopsy providing enough material for formalin-fixed samples. Core biopsies may be appropriate as the only diagnostic test in the rare patients requiring emergency treatment. Minimal immunohistochemistry (CD45, CD20 and CD3) is mandatory. The collection of fresh frozen material for molecular characterization is recommended although gene expression profiling remains investigational. To ensure adequate quality, processing by an experienced pathology institute has to be guaranteed. The histological report should give the diagnosis according to the current World Health Organization classification.
Size reversion of African cassava mosaic virus coat protein gene deletion mutants during infection of Nicotiana benthamiana.

Mutants of African cassava mosaic virus containing extensive deletions across the coat protein gene that remove up to one-third of the genomic component have been constructed and shown to be infectious when mechanically inoculated onto Nicotiana benthamiana by leaf abrasion. Using N. tabacum protoplasts we demonstrate that mutant pCLV.CP delta 11, containing a 712 bp deletion, is competent for replication in its deleted form. However, systemic spread of pCLV. CP delta 11 and other deletion mutants is associated with reversion of DNA 1 to a size comparable to that of the native genomic component. This contrasts with the behaviour of coat protein mutants of the closely related geminivirus tomato golden mosaic virus which maintain their deletions during spread. Appraisal of the different inoculation procedures used to introduce the mutants into plants suggests the imposition of a stringent size requirement for localized cell-to-cell spread which is relaxed for long distance spread through the vascular system.
Harmonic components based protection strategy for inverter-interfaced AC microgrid

In the inverter-interfaced AC microgrid (IIAM), when a short-circuit fault occurs at the distribution line, the output fault current of inverter is commonly limited to two times over its rated current due to the limited overcurrent capacity of power electronic device. Therefore, the conventional overcurrent protection principle cannot be applied to IIAM. Aiming at addressing this issue, a new protection method based on the low harmonics components is proposed in this paper. Through injecting a certain proportion of fifth harmonics to the fault current, the protection device can detect the fault according to the low harmonics components extracted by the digital relay (DR). This scheme does not rely on the large fault current. Therefore, some limitations of the traditional overcurrent protection are avoided. The corresponding experiments were carried out with two 10kVA parallel-connected inverters supply system, and the results proved the feasibility of this approach.
Functional Roles for the Pleckstrin and Dbl Homology Regions in the Ras Exchange Factor Son-of-sevenless (*)

Activation of p21 by receptor tyrosine kinases is thought to result from recruitment of guanine nucleotide exchange factors such as Son-of-sevenless (Sos) to plasma membrane receptor substrates via adaptor proteins such as Grb2. This hypothesis was tested in the present studies by evaluating the ability of truncation and deletion mutants of Drosophila (d)Sos to enhance [P]GTP loading of p21 when expressed in P-labeled COS or 293 cells. The dSos catalytic domain (residues 758-1125), expressed without the dSos NH2-terminal (residues 1-757) or adaptor-binding, COOH-terminal (residues 1126-1596) regions, exhibits intrinsic exchange activity as evidenced by its rescue of mutant Saccharomyces cerevisiae deficient in endogenous GTP/GDP exchange activity. Here we show that this dSos catalytic domain fails to affect GTPp21 levels when expressed in cultured mammalian cells unless the NH2-terminal domain is also present. Surprisingly, the COOH-terminal, adaptor binding domain of dSos was not sufficient to confer p21 exchange activity to the Sos catalytic domain in these cells in the absence of the NH2-terminal domain. This function of promoting catalytic domain activity could be localized by mutational analysis to the pleckstrin and Dbl homology sequences located just NH2-terminal to the catalytic domain. The results demonstrate a functional role for these pleckstrin and Dbl domains within the dSos protein, and suggest the presence of unidentified cellular elements that interact with these domains and participate in the regulation of p21.
Hemagglutinating Activity of Gallibacterium Strains

Abstract In the present study, the hemagglutinating activity of seven reference strains, and nine Mexican and three Danish field isolates, of Gallibacterium was investigated by using fresh erythrocytes of 19 different types including chicken (broiler, rooster, layer hen), turkey, pigeon, quail, duck, Harris's hawk (Parabuteo unicinctus), house finch (Carpodacus mexicanus), cow, sheep, horse, dog, rabbit, pig, and human (groups A, B, AB, and O; Rh+). Agglutination was observed for broiler chicken, layer hen, quail, rabbit, and pig erythrocytes with a subset of Gallibacterium strains, whereas most tested strains agglutinated rabbit erythrocytes. Transmission electron microscopic examination of a hemagglutinating strain demonstrated a close interaction between the bacterial and erythrocyte surfaces. The results indicate that some Gallibacterium strains are able to agglutinate avian or mammalian erythrocytes, or both. However, the mechanisms enabling hemagglutination are not known and will be addressed in future studies.
Exploring Generalized Association Rule Mining for Disease Co-Occurrences

Association rule mining offers an automated approach for discovering new knowledge about diseases. A known challenge is how to constrain the search space to prevent an exponential explosion of rules while minimizing information loss. In this study, generalized association rule mining techniques were used to identify disease cooccurrences based on ICD-9-CM codes in a statewide hospital discharge data set. The Clinical Classifications Software (CCS) categorization scheme and the numerical hierarchy of ICD-9-CM were used to generalize the codes and produce generalized associations for comparison with associations generated from the raw data. By maintaining links between the raw and generalized data, associations lost in the generalization process, overlapping associations, and new associations were identified. In addition, preliminary results indicate that the concept hierarchy used for generalization may influence the associations found.
Atherosclerosis: Current concepts on pathogenesis and interventional therapies

Atherosclerosis, the primary pathological condition accounting for most stroke syndromes, has been the intense focus of epidemiological, basic, and clinical investigations. Since these studies have direct bearing on the prevention of atherothrombotic brain infarction, this review emphasizes those advances in treatment resulting from their findings. The two most prominent theories on the pathogenesis of atherosclerosis relate to aberrations in lipoprotein metabolism and to enhanced proliferation of smooth muscle cells; likely, the theories are complementary. As a practical guideline for preventive therapy, the importance of using the total cholesterol level is stressed, although finer distinctions must rely on the low‐density and high‐density lipoprotein concentrations and their normalization. Since prevention of stroke may ultimately be its most effective therapy, consideration of cholesterol level, akin to strategies for preventing coronary heart disease, and efforts to avert platelet adhesion or aggregation and coagulation are warranted.
A Relevancy Filter for Constructive Induction

Some machine-learning algorithms enable the learner to extend its vocabulary with new terms if, for a given a set of training examples, the learner's vocabulary is too restricted to solve the learning task. We propose a filter, called the Reduce algorithm, that selects potentially relevant terms from the set of constructed terms and eliminates terms that are irrelevant for the learning task. Restricting constructive induction (or predicate invention) to relevant terms allows a much larger explored space of constructed terms. The elimination of irrelevant terms is especially well-suited for learners of large time or space complexity, such as genetic algorithms and artificial neural networks. To illustrate our approach to feature construction and irrelevant feature elimination, we applied our proposed relevancy filter to the 20- and 24-train East-West Challenge problems. The experiments show that the performance of a hybrid genetic algorithm, RL-ICET (Relational Learning with ICET), improved significantly when we applied the relevancy filter while pre-processing the data set.
Non-linear Continuous Systems for Safety Verification

Safety verification of hybrid dynamical systems relies crucially on the ability to reason about reachable sets of continuous systems whose evolution is governed by a system of ordinary differential equations (ODEs). Verification tools are often restricted to handling a particular class of continuous systems, such as e.g. differential equations with constant right-hand sides, or systems of affine ODEs. More recently, verification tools capable of working with non-linear differential equations have been developed. The behavior of non-linear systems is known to be in general extremely difficult to analyze because solutions are rarely available in closed-form. In order to assess the practical utility of the various verification tools working with non-linear ODEs it is very useful to maintain a set of verification problems. Similar efforts have been successful in other communities, such as automated theorem proving, SAT solving and numerical analysis, and have accelerated improvements in the tools and their underlying algorithms. We present a set of 65 safety verification problems featuring non-linear polynomial ODEs and for which we have proofs of safety. We discuss the various issues associated with benchmarking the currently available verification tools using these problems.
Expression and gene variation studies deny association of human HSD3B1 gene with aldosterone production or blood pressure.

BACKGROUND Recent evidence suggests that the type I 3β-hydroxysteroid dehydrogenase, a steroidogenic enzyme encoded by the HSD3B1 gene, could be involved in aldosterone production and that genetic variation in HSD3B1 is associated with blood pressure. These findings challenge the long-standing hypothesis that all adrenocortical steroidogenesis is executed by the type II iso-enzyme, encoded by HSD3B2. METHODS To verify these findings, the adrenal presence of HSD3B1 and its effect on aldosterone synthesis and blood pressure were studied in expression and genetic association analyses, respectively. Expression of HSD3B1 and HSD3B2 was investigated in various adrenocortical tissues (n = 15) and in primary adrenal cell cultures (n = 5) after stimulation with adrenocorticotropin and angiotensin II. Six tagging single nucleotide polymorphisms within the HSD3B1 gene were studied for association with blood pressure and hypertension in a meta-analysis of 4 Dutch cohorts (n = 11,192). RESULTS HSD3B1 expression was minimal or absent in adrenocortical tissues, including 6 aldosterone-producing adenomas. In contrast with the ubiquitously expressed HSD3B2 mRNA, HSD3B1 levels were not stimulated by adrenocorticotropin or angiotensin II. No variants in the HSD3B1 gene were associated with blood pressure or the occurrence of hypertension. CONCLUSIONS We found no evidence to support confirmation that HSD3B1 is involved in aldosterone synthesis in the human adrenal cortex or that genetic variation in HSD3B1 affects blood pressure or hypertension, favoring the hypothesis that all adrenocortical steroidogenesis is primarily dependent on the type II 3β-hydroxysteroid dehydrogenase.
Novel Enamine Derivatives of 5,6-Dihydro-2′-Deoxyuridine Formed in Reductive Amination of 5-Formyl-2′-Deoxyuridine

Reductive amination of 5-formyl-3′,5′-di-O-acetyl-2′-deoxyuridine with primary amines and sodium triacetoxyborohydride (NaBH(OAc)3) afforded novel enamine derivatives of 5,6-dihydro-2′-deoxyuridine as a result of unexpected 1,4-conjugate reduction of intermediate Schiff bases in addition to the secondary amine derivatives of 2′-deoxyuridine, typical 1,2-reduction products.
Are We Too Pessimistic about Drug-Resistant Epilepsy?

median follow-up from the onset of adequate medication before the age of 16 years, 84 (82%) of 102 patients with incident drug-resistant epilepsy eventually entered one or more 1-year remissions, 81 (79%) one or more 2-year remissions, 70 (69%) one or more 5-year remissions and 52 (51%) of 102 5-year terminal remissions. In contrast, 18 (18%) of 102 patients with incident drug-resistant epilepsy never entered any 1-year remission, 21 (21%) 2-year remission, 32 (31%) 5-year remission and 50 (49%) of 102 any 5-year terminal remission. On multivariate analysis of clinical features, in every remission category, idiopathic or cryptogenic aetiology was the only significant predictor of entering remission. Incident drug-resistant epilepsy is eventually reversible in 49–79% of patients with mostly focal epilepsy, resulting in long-term remission of variable duration. Idiopathic or cryptogenic aetiology is a clinical predictor of reversible drug-resistant epilepsy.