Miracle-dz/UniFAR-FTUs huggingface dataset:
Measure Twice, Estimate Once: Pacific Salmon Population Viability Analysis for Highly Variable Populations

Abstract Because many stocks of Pacific salmon Oncorhynchus spp. are listed under the U.S. Endangered Species Act (ESA), research has focused on predicting the future population dynamics for these low-abundance stocks. One method used to make predictions is known as population viability analysis. Pacific salmon populations exhibit much higher apparent variability than other ESA-listed vertebrates, and high variability increases the probability of extinction. If the high variability is primarily due to counting methods, it could be reduced in model predictions by using methods that correct for measurement error, sampling error, or both. Using data from British Columbia pink salmon O. gorbuscha and Snake River spring- or summer-run Chinook salmon O. tshawytscha and several modeling approaches (Ricker, Dennis, and state-space models), we compared repeated counts of the same population (e.g., spawner and fry, dam and redd counts). We applied the methods to the first half of the time series and compared the pr.
Association study of the NF1 gene and autistic disorder.

Neurofibromatosis type 1 (NF1) is increased about 150-fold in autistic patients. The aim of this study was to test for an association between the NF1 locus and autistic disorder. The allele distributions of three markers of the NF1 gene were studied in 85 autistic patients and 90 controls. No differences in allele distributions were observed. However, we found a new allele (allele 5) of the GXAlu marker in four autistic patients. Allele 5 was absent in a larger control population (213 individuals). The patients with allele 5 had a more severe clinical picture, mainly in the fields of motility and tonus. Our preliminary results suggest that the NF1 region is not a major susceptibility locus for autism. However, the GXAlu marker of the NF1 gene appears as a possible candidate for a susceptibility locus in a small subgroup of severely affected autistic patients. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:729-732, 1999.
Self-care agency and symptom management in patients treated for mood disorder.

Symptom management of patients with mood disorder, such as depression and bipolar disorder, influences quality of life and relapse. This article describes a study of symptom recognition and management and the ability of self-care agency to predict symptom management. A purposive sample of 45 subjects was studied. Step-wise multiple regression analyses of self-care agency with symptom management resulted in self-care agency explaining 37% of the variance in symptom management at 2 months posthospitalization. Patients with mood disorders have long-term vulnerability for relapse after hospital stabilization. Nurses need to continue to find ways to assess and strengthen symptom management and self-care in these relapse-prone individuals.
The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence.

This review represents an update of the nomenclature system for the UDP glucuronosyltransferase gene superfamily, which is based on divergent evolution. Since the previous review in 1991, sequences of many related UDP glycosyltransferases from lower organisms have appeared in the database, which expand our database considerably. At latest count, in animals, yeast, plants and bacteria there are 110 distinct cDNAs/genes whose protein products all contain a characteristic 'signature sequence' and, thus, are regarded as members of the same superfamily. Comparison of a relatedness tree of proteins leads to the definition of 33 families. It should be emphasized that at least six cloned UDP-GlcNAc N-acetylglucosaminyltransferases are not sufficiently homologous to be included as members of this superfamily and may represent an example of convergent evolution. For naming each gene, it is recommended that the root symbol UGT for human (Ugt for mouse and Drosophila), denoting 'UDP glycosyltransferase,' be followed by an Arabic number representing the family, a letter designating the subfamily, and an Arabic numeral denoting the individual gene within the family or subfamily, e.g. 'human UGT2B4' and 'mouse Ugt2b5'. We recommend the name 'UDP glycosyltransferase' because many of the proteins do not preferentially use UDP glucuronic acid, or their nucleotide sugar preference is unknown. Whereas the gene is italicized, the corresponding cDNA, transcript, protein and enzyme activity should be written with upper-case letters and without italics, e.g. 'human or mouse UGT1A1. ' The UGT1 gene (spanning > 500 kb) contains at least 12 promoters/first exons, which can be spliced and joined with common exons 2 through 5, leading to different N-terminal halves but identical C-terminal halves of the gene products; in this scheme each first exon is regarded as a distinct gene (e.g. UGT1A1, UGT1A2, . UGT1A12). When an orthologous gene between species cannot be identified with certainty, as occurs in the UGT2B subfamily, sequential naming of the genes is being carried out chronologically as they become characterized. We suggest that the Human Gene Nomenclature Guidelines (http://www.gene.acl.ac.uk/nomenclature/guidelines.html++ +) be used for all species other than the mouse and Drosophila. Thirty published human UGT1A1 mutant alleles responsible for clinical hyperbilirubinemias are listed herein, and given numbers following an asterisk (e.g. UGT1A1*30) consistent with the Human Gene Nomenclature Guidelines. It is anticipated that this UGT gene nomenclature system will require updating on a regular basis.
Two Classes of Plant cDNA Clones Differentially Complement Yeast Calcineurin Mutants and Increase Salt Tolerance of Wild-type Yeast*

The salt-sensitive phenotype of yeast cells deficient in the phosphoprotein phosphatase, calcineurin, was used to identify genes from the higher plant Arabidopsis thaliana that complement this phenotype. cDNA clones corresponding to two different sequences, designated STO (salt tolerance) and STZ (salt tolerance zinc finger), were found to increased tolerance of calcineurin mutants and of wild-type yeast to both Li+ and Na+ ions. STZ is related to Cys2/His2-type zinc-finger proteins found in higher plants, and STO is similar to the Arabidopsis CONSTANS protein in regions that may also be zinc fingers. Although neither protein has sequence similarity to any protein phosphatase, STO was able to at least partially compensate for all tested additional phenotypic effects of calcineurin deficiency, and STZ compensated for a subset of these effects. Salt tolerance produced by STZ appeared to be partially dependent on ENA1/PMR2, a P-type ATPase required for Li+ and Na+ efflux in yeast, whereas the effect of STO on salt tolerance was independent of ENA1/PMR2. STZ and STO were found to be expressed in Arabidopsis roots and leaves, whereas only STO message was detectable in flowers. An apparent increase in the level of STZ mRNA was observed in response NaCl exposure in Arabidopsis seedlings, but the level of STO mRNA was not altered by this treatment.
Eosinophils and Cancer – Mini Review

The focus of this review is to discuss the role of eosinophils in cancer. A study published in the Journal of Clinical Oncology examined the relationship between eosinophils in peripheral blood and the incidence of colorectal cancer [2]. The researchers found that a higher number of peripheral blood eosinophils were associated with a reduced risk of dying from colorectal cancer, especially in patients who never smoked and in males. Although the study could not identify the mechanism to explain this relationship, one plausible theory is that a more active immune system reduces the risk of developing colorectal cancer. Another study published in the journal Modern Pathology in 2016. Prizement et al. [3] looked at how eosinophils might predict outcomes for patients with colorectal cancer. Taghizadeh et al. [4] found no associations between objective allergy markers and cancer in a total population but reported positivity and a high number of eosinophils with association to reduced risk to die of cancer in specific subgroups. Although staging of colorectal cancer typically is based on information about the tumor itself, lymph node involvement, and the presence of metastases (cancer spread to other sites), often two patients with the same staging will have dramatically different outcome. The authors of this study examined whether eosinophils levels in or around a colorectal tumor helps predict outcome. They concluded that a higher numbers of eosinophils around the primary colorectal tumor were associated with an improved patient outcome, and that they should be routinely counted during tumor examination, it was found that the infiltration of tumors with eosinophils, especially in stromal tissue, may be an important prognostic factor in colorectal cancer.
The Role of Trait Anxiety in the Interaction between Eye Gaze and Facial Expressions

Previous research revealed an interaction between eye gaze and emotional facial expressions. There are also evidences that elevated levels of trait anxiety are associated with an increased ability to accurately recognize facial expressions of fear, and enhanced cueing effect of eye gaze of fearful faces. In this study, we investigate the relationship between facial expression and gaze processing with the Garner selective attention paradigm, taking individual differences in trait anxiety into account. Results indicated that facial expression interferes with eye gaze judgments, but gaze does not influence perception of facial expressions. These findings were not stimulus-bound. Furthermore, no anxiety-related differences in the interactions were found. Thus, our study reveals that anxiety does not play an important role in the interaction between eye gaze and facial expressions. Previous findings that anxiety may facilitate cuing effect of gaze direction of fear faces might be task-bound.
Supportive periodontal therapy.

A case-control study comparing the efficacy a 2% minocycline gel versus scaling and root planing (SRP) alone, in treating with pocket greater than or equal to 5 mm, with bleeding on probing during a 12- month period of maintenance care, resulted in similar clinical outcome. Similar results have been found with the adjunctive use of a 25% metronidazole gel in combination with SRP.
Somatostatin, pancreatic polypeptide, substance P, and neurotensin: cellular distribution and effects on stimulated insulin secretion in the mouse.

Somatostatin, pancreatic polypeptide (PP), substance P1 and neurotensin were investigated in mice with regard to their cellular localization in gut and pancreas and their effects on stimulated insulin secretion. Immunohistochemical demonstration of the different peptides revealed the following distribution. PP cells were confined to the pancreatic islets where they seemed to be in close association with the glucagon cells. They were especially abundant in the duodenal part of the pancreas. Somatostatin cells were found in pancreatic islets as well as throughout the gastrointestinal tract. In contrast to PP cells, somatostatin and glucagon cells were more numerous in the splenic part of the pancreas. Scattered endocrine cells displaying substance P immunoreactivity were found mainly in the duodenum, whereas neurotensin cells predominated in the jejuno-ileum. In addition, substance P immunoreactivity was demonstrated in nerves of the intestinal wall. Neither substance P cells nor neurotensin cells could be .
Prognostic Factors in Patients with Pathologic T1-2N1M0 Disease in Non-small Cell Carcinoma of the Lung

Introduction: Patients with stage II non-small cell lung carcinoma (NSCLC) represent a heterogeneous subgroup with variable 5-year survival rates. The influence of the type of lymph node involvement on survival and recurrence was investigated. Methods: A total of 128 consecutive patients who underwent complete tumor resection and mediastinal lymph nodes dissection for pT1-2N1M0 NSCLC between July 1991 and December 2003 were retrospectively reviewed. Results: The overall 5-year survival of patients with T1-2N1M0 disease was 42.2%. Although pT status, histology, surgical procedure, and adjuvant therapy did not affect survival for pT1-2N1M0 patients, the 5-year survival rate differed significantly according to the type of lymph node involvement. The 5-year survival rate for patients with main bronchial lymph node involvement, interlobar and lobar lymph node involvement, and segmental bronchial lymph node involvement was 19.7%, 39.8%, and 59.7%, respectively. The survival curves of these three groups had significant differences. Fifty-five patients had cancer recurrence, and the type of lymph node involvement did not affect the pattern of cancer relapse. Conclusions: In patients with stage II NSCLC, survival differs according to the type of lymph node involvement: patients with only segmental lymph node involvement have a better prognosis and the disease seems to be at an early stage, whereas patients with main bronchial lymph node involvement have a poorer prognosis, and main bronchial lymph node involvement represents more advanced disease. Patients with pN1 disease represent a heterogeneous group that may be subdivided according to the level of the involved N1 station, not pT factor.
Decision Dynamics in Groups with Interacting Members

Group decisions involve the combination of evidence accumulation by individual members and direct member-to-member interactions. We consider a simplified framework of two deciders, each undergoing a two alternative forced choice task, with the choices of early deciding members biasing members who have yet to choose. We model decision dynamics as a drift-diffusion process and present analysis of the associated Fokker--Planck equation for the group. We show that the probability of coordinated group decisions (both members make the same decision) is maximized by setting the decision threshold of one member to a lower value than its neighbor's. This result is akin to a speed-accuracy tradeoff, where the penalty of lowering the decision threshold is choice inaccuracy while the benefit is that earlier decisions have a higher probability of influencing the other member. We numerically extend these results to large group decisions, where it is shown that by choosing the appropriate parameters, a small but decisiv.
Nuclear Survivin Is Associated With Malignant Potential in Epithelial Ovarian Carcinoma

Survivin is a unique member of the inhibitor of apoptosis (IAP) protein family. As abnormal inhibition of apoptosis during homeostasis is considered a critical step in the initiation of cancer, we investigated prognostic value of survivin expression in epithelial ovarian carcinomas. We carried out immunohistochemical experiments using a polyclonal antisurvivin antibody to stain formalin-fixed paraffin-embedded sections from 91 patients with ovarian tumors, including 10 cystadenomas, 17 borderline tumors, and 64 epithelial ovarian carcinomas. Nuclear and cytoplasmic survivin staining was scored separately. Survivin expression was undetectable in ovarian cystadenomas and was weakly detected in 4 of 17 (23.53%) borderline tumors. In contrast, nuclear and cytoplasmic survivin staining was observed in 55 of 64 (85.94%) epithelial ovarian carcinomas. Scoring on the basis of the percentage of survivin nuclear-positive cells indicated that nuclear survivin expression was associated significantly with clinical stage, histologic grade, proliferating cell nuclear antigen (PCNA)-labeling index, and clinical outcome in ovarian epithelial carcinoma patients (P<0.01). Taken together, the results of this study provide evidence that nuclear survivin expression is a strong, independent prognostic marker for poor clinical outcomes in epithelial ovarian carcinoma.
Paradox of a graduate human science curriculum experienced online: a faculty perspective.

BACKGROUND Program evaluation contributes to evidence-based nursing education. Exploring graduate faculty experience with developing and teaching an online master's of science in nursing program contributes to building a science of nursing education. METHODS A multimodal methodology for conducting a program evaluation is participatory and demonstrates both formative (improve the quality of the program) and summative (determine the worth of the program) components. Faculty participated through questionnaires, journals, and focus groups. RESULTS In the context of a philosophy that values understanding lived experience as foundational for nursing, faculty are teaching in an environment that is disembodied, technology based, and at a distance. Faculty relationships with students reveal emerging curricular issues. CONCLUSIONS Research into the intersection of pedagogy and technology reveals similarities with contemporary literature and many lived paradoxes to be accounted for in evaluation of graduate nursing education.
Fewer protective cytotoxic T-cell epitopes than T-helper-cell epitopes on vesicular stomatitis virus

Cytotoxic T-lymphocyte (CTL) and T-helper-cell responses in various mouse strains were monitored. Protective CTL responsiveness against three proteins of vesicular stomatitis virus was H-2 linked and inducible only in half of the 15 combinations tested (each of five H-2 haplotypes combined with each of three viral proteins), whereas biologically relevant T-helper-cell responses were inducible in all. This suggests that vesicular stomatitis virus exhibits more T-helper-cell than CTL epitopes.
Decreased KCNE 2 Expression Participates in the Development of Cardiac Hypertrophy by Regulation of Calcineurin – NFAT ( Nuclear Factor of Activated T Cells ) and Mitogen-Activated Protein Kinase Pathways

1 Cardiac hypertrophy is an adaptive response to pathological stimuli to preserve contractility and cardiac function. However, prolonged hypertrophy leads to maladaptive structural and functional remodeling and is associated with a significant increase in the risk for serious conditions, including arrhythmias, sudden death, and heart failure (HF). The pathological hypertrophic development involves multiple intracellular signaling pathways, including enhancement of calcium-regulated signaling pathways. Among them, the most extensively studied is calcineurin transcriptional NFAT (nuclear factor of activated T cells) pathway. Calcineurin, a serine threonine protein phosphatase, is activated by calcium/calmodulin under various prohypertrophic stimuli, including αand β-adrenergic agonists, angiotensin II, and endothelin-1. On dephosphorylation by calcineurin, NFAT translocates to the nucleus of the cardiomyocyte where it mediates the transcription of numerous targets involved Original Article
Targeting protein–protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies?

Over the past several years, there has been an increasing research effort focused on inhibition of protein–protein interactions (PPIs) to develop novel therapeutic approaches for cancer, including hematologic malignancies. These efforts have led to development of small molecule inhibitors of PPIs, some of which already advanced to the stage of clinical trials while others are at different stages of preclinical optimization, emphasizing PPIs as an emerging and attractive class of drug targets. Here, we review several examples of recently developed inhibitors of PPIs highly relevant to hematologic cancers. We address the existing skepticism about feasibility of targeting PPIs and emphasize potential therapeutic benefit from blocking PPIs in hematologic malignancies. We then use these examples to discuss the approaches for successful identification of PPI inhibitors and provide analysis of the protein–protein interfaces, with the goal to address ‘druggability’ of new PPIs relevant to hematology. We discuss lessons learned to improve the success of targeting new PPIs and evaluate prospects and limits of the research in this field. We conclude that not all PPIs are equally tractable for blocking by small molecules, and detailed analysis of PPI interfaces is critical for selection of those with the highest chance of success. Together, our analysis uncovers patterns that should help to advance drug discovery in hematologic malignancies by successful targeting of new PPIs.
Heparan Sulfate-Binding Foot-and-Mouth Disease Virus Enters Cells via Caveola-Mediated Endocytosis

ABSTRACT Foot-and-mouth disease virus (FMDV) utilizes different cell surface macromolecules to facilitate infection of cultured cells. Virus, which is virulent for susceptible animals, infects cells via four members of the αV subclass of cellular integrins. In contrast, tissue culture adaptation of some FMDV serotypes results in the loss of viral virulence in the animal, accompanied by the loss of virus' ability to use integrins as receptors. These avirulent viral variants acquire positively charged amino acids on surface-exposed structural proteins, resulting in the utilization of cell surface heparan sulfate (HS) molecules as receptors. We have recently shown that FMDV serotypes utilizing integrin receptors enter cells via a clathrin-mediated mechanism into early endosomes. Acidification within the endosome results in a breakdown of the viral capsid, releasing the RNA, which enters the cytoplasm by a still undefined mechanism. Since there is evidence that HS internalizes bound ligands via a caveola-mediated mechanism, it was of interest to analyze the entry of FMDV by cell-surface HS. Using a genetically engineered variant of type O1Campos (O1C3056R) which can utilize both integrins and HS as receptors and a second variant (O1C3056R-KGE) which can utilize only HS as a receptor, we followed viral entry using confocal microscopy. After virus bound to cells at 4°C, followed by a temperature shift to 37°C, type O1C3056R-KGE colocalized with caveolin-1, while O1C3056R colocalized with both clathrin and caveolin-1. Compounds which either disrupt or inhibit the formation of lipid rafts inhibited the replication of O1C3056R-KGE. Furthermore, a caveolin-1 knockdown by RNA interference also considerably reduced the efficiency of O1C3056R-KGE infection. These results indicate that HS-binding FMDV enters the cells via the caveola-mediated endocytosis pathway and that caveolae can associate and traffic with endosomes. In addition, these results further suggest that the route of FMDV entry into cells is a function solely of the viral receptor.
Delusional Disorders : An Overview

In recent years, delusional disorders have emerged as a focus of clinical research and treatment innovation. Despite these advances, clinicians are still relatively ill informed about this group of disorders. The present review tries to update on historical aspects, current nosology, epidemiology, validity of the concept and treatment strategies for the delusional disorders. Over the years the concept of delusional disorders has been changing and has still not crystallized fully. The variation in diagnostic criteria over the years has hampered research in this field. The available research is mostly retrospective, with control groups of schizophrenia, and focusing more on demographic variables than the illness, treatment and outcome variables. There is a need for prospective studies with a variety of control groups and focus on a wide array of parameters that can help to validate delusional disorders as an independent diagnostic entity (German J Psychiatry 2006;9:62-73).