gebhart/patrepeval huggingface dataset:
Social pairing and female mating fidelity predicted by restriction fragment length polymorphism similarity at the major histocompatibility complex in a songbird (2003)

Female birds often copulate outside the pair-bond to produce broods of mixed paternity, but despite much recent attention the adaptive significance of this behaviour remains elusive. Although several studies support the idea that extra-pair copulations (EPCs) allow females to obtain 'good genes' for their offspring, many others have found no relationship between female mating fidelity and traits likely to reflect male quality. A corollary to the good genes hypothesis proposes that females do use EPCs to increase the quality of young, but it is the interaction between maternal and paternal genomes - and not male quality per se - that is the target of female choice. We tested this 'genetic compatibility' hypothesis in a free-living population of Savannah sparrows (Passerculus sandwichensis) by determining whether females mated nonrandomly with respect to the major histocompatibility complex (Mhc). During both the 1994 and 1995 breeding seasons, female yearlings (but not older birds) avoided pairing with Mhc-similar males (P < 0.005). The Mhc similarity between mates also predicted the occurrence of extra-pair young in first broods (P < 0.007) and covaried with estimates of genome-wide levels of similarity derived from multilocus DNA fingerprinting profiles (P = 0.007). The overall genetic similarity between adults tended to predict female mating fidelity, but with less precision than their Mhc similarity (P = 0.09). In contrast, females appeared insensitive to the size, weight or age of males, none of which explained variation in female mating fidelity. Taken together, these results are consistent with the hypothesis that females sought complementary genes for their offspring and suggest either that the benefits of heterozygosity (at the Mhc) drive female mating patterns or that the avoidance of inbreeding is an ultimate cause of social and genetic mate choice in Savannah sparrows.
Novel mutations in the FOXC1 gene in Japanese patients with Axenfeld-Rieger syndrome. (2007)

A novel mutation in Helix1 and a novel deletion in Wing1 and Beta2 of the forkhead domain of the FOXC1 gene have been identified in two families with ARS. FOXC1 mutations cause a variety of developmental abnormalities in the anterior segment of the eye, and they also induce an elevation in intraocular pressures and early-onset glaucoma.
Intraparotid lymph node with metastatic angiosarcoma: A rare tumor with a routine presentation (2012)

We present an unusual case presenting as a parotid tumor in a Caucasian man, including our management and a review of literature. Case Report: A 83-year-old male was referred to the ENT department with a nonpainful swelling in front of his right ear. This was diagnosed as a likely Warthin's tumor and this was further supported by ultrasound imaging. Fine needle aspiration cytology was non-diagnostic. The patient underwent superficial parotidectomy for histological confirmation. Histology identified an intraparotid lymph node with metastatic angiosarcoma. The primary source was not identified. The patient was further treated with adjuvant radiotherapy and at a to-month posttherapy review there is no evidence of reoccurrence. Conclusion: An angiosarcoma is a rare malignant neoplasm of endothelial-type that is characterized by rapidly proliferating and infiltrating anaplastic cells. Angiosarcoma's account for less than 0.1% of all head and neck cancers and it is extremely rare for the major salivary glands to be affected; 80% of all parotid tumors are benign. Metastatic angiosarcoma arising in an intraparotid lymph node has not previously been reported in English journals. This presented case is unusual in its location and its mode of presentation.
Systematic Review of the Military Career Impact of Mental Health Evaluation and Treatment (2021)

Despite considerable efforts to destigmatize MH treatment-seeking, a substantial proportion of service members believe that seeking help will negatively impact their careers. On one hand, these perceptions are somewhat backed by reality, as seeking MH treatment is associated with a higher likelihood of being involuntarily discharged. On the other hand, correlational designs cannot establish causality. Variables that increase both treatment-seeking and discharge could include (1) adverse childhood experiences; (2) elevated psychological problems (including both [a] the often-screened depression, anxiety, and posttraumatic stress problems and [b] problems that can interfere with military service: personality disorders, psychotic disorders, and bipolar disorder, among others); (3) a history of aggressive or behavioral problems; and (4) alcohol use and abuse. In addition, most referrals are self-directed and do not result in any career-affecting provider recommendations. In conclusion, the essential question of this research area-"Does seeking MH treatment, compared with not seeking treatment, cause career harm?"-has not been addressed scientifically. At a minimum, longitudinal studies before treatment initiation are required, with multiple data collection waves comprising symptom measurement, treatment, and other services obtained, and a content-valid measure of career impact.
Synthetic Biology of Proteins: Tuning GFPs Folding and Stability with Fluoroproline (2008)

We discovered that the folding rates and stability of GFP are affected to a lesser extent by cis/trans isomerization of the proline bonds than by the puckering of pyrrolidine rings. In the C(gamma)-endo conformation the fluorine atoms are positioned in the structural context of the GFP such that a network of favorable local interactions is established. From these results the combined use of synthetic amino acids along with detailed structural knowledge and existing protein engineering methods can be envisioned as a promising strategy for the design of complex tailor-made proteins and even cellular structures of superior properties compared to the native forms.
Positive and Negative Regulation of <i>Tetrahymena</i> Telomerase Holoenzyme (2007)

Telomerase replenishes the telomeric repeats that cap eukaryotic chromosome ends. To perform DNA synthesis, the active site of telomerase reverse transcriptase (TERT) copies a template within the integral telomerase RNA (TER). In vivo, TERT and TER and additional subunits form a telomerase holoenzyme capable of telomere elongation. We previously purified epitope-tagged Tetrahymena thermophila TERT and characterized two of the associated proteins. Here we characterize the remaining two proteins that were enriched by TERT purification. The primary sequence of the p75 polypeptide lacks evident homology with other proteins, whereas the p20 polypeptide is the Tetrahymena ortholog of a conserved multifunctional protein, Skp1. Genetic depletion of p75 induced telomere shortening without affecting the accumulation of TER or TERT, suggesting that p75 promotes telomerase function at the telomere. Affinity purification of p75 coenriched telomerase activity and each other known telomerase holoenzyme protein. On the other hand, genetic depletion of Skp1p induced telomere elongation, suggesting that this protein plays a negative regulatory role in the maintenance of telomere length homeostasis. Affinity purification of Skp1p did not detectably enrich active telomerase but did copurify ubiquitin ligase machinery. These studies reveal additional complexity in the positive and negative regulation of Tetrahymena telomerase function.
Molecular architecture and rheological characterization of novel intramolecularly crosslinked polystyrene nanoparticles (2006)

Abstract Novel polystyrene nanoparticles were synthesized by the controlled intramolecular crosslinking of linear polymer chains to produce well‐defined single‐molecule nanoparticles of varying molecular mass, corresponding directly to the original linear precursor chain. These nanoparticles are ideal to study the relaxation dynamics/processes of high molecular mass polymer melts, as the high degree of intramolecular crosslinking potentially inhibits entanglements. Both the nanoparticles and their linear analogs were characterized by measuring their intrinsic viscosity, hydrodynamic radius ( R h ), and radius of gyration ( R g ). The ratio R g / R h was computed to characterize the molecular architecture of the nanoparticles in solution, revealing a shift toward the constant density sphere limit with increasing crosslink density and molecular mass. Further, confirming particulate behavior, Kratky plots obtained from neutron scattering data show a shift toward particle‐like nature. The rheological behavior of the particles was found to be strongly dependent on both the extent of intramolecular crosslinking and molecular mass, with a minimal viscosity change at low crosslinking levels and a gel‐like behavior evident for a large degree of crosslinking. These and other results suggest the presence of a secondary mode of polymer relaxation/movement besides reptation, which in this case, is influenced by the total number of crosslinked loops present in the nanoparticle. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1930–1947, 2006
Interaction Techniques for Navigation through and Manipulation of 2D and 3D Data (2002)

In this article we present a working prototype incorporating some new interaction techniques for the navigation through and the manipulation of both 3D and 2D data. The prototype aims at professional applications like architectural design, surgical planning and geological exploration. Its design was influenced by the analysis of user requirements and by the requirement for a natural interface. The prototype permits the user to navigate through 3D and 2D data in order to explore the internal structure. 3D navigation is accomplished by means of a natural selection of dynamically updated cross-sections. The user can navigate through these selected cross-sections of 2D data and can perform manipulations with them. As a proof of concept we focus on two disciplines, viz. architectural design and surgical planning. Our usability evaluation of the interaction styles demonstrates that they are perceived as useful and enjoyable additions to existing techniques in these disciplines.
Gads‐deficient thymocytes are blocked at the transitional single positive CD4<sup>+</sup> stage (2009)

Positive selection of T-cell precursors is the process by which a diverse T-cell repertoire is established. Positive selection begins at the CD4(+)CD8(+) double positive (DP) stage of development and involves at least two steps. First, DP thymocytes down-regulate CD8 to become transitional single positive (TSP) CD4(+) thymocytes. Then, cells are selected to become either mature single positive CD4(+) or mature single positive CD8(+) thymocytes. We sought to define the function of Gads during the two steps of positive selection by analyzing a Gads-deficient mouse line. In Gads(+/+) mice, most TSP CD4(+) thymocytes are TCR(hi)Bcl-2(hi)CD69(+), suggesting that essential steps in positive selection occurred in the DP stage. Despite that Gads(-/-) mice could readily generate TSP CD4(+) thymocytes, many Gads(-/-) TSP CD4(+) cells were TCR(lo)Bcl-2(lo)CD69(-), suggesting that Gads(-/-) cells proceeded to the TSP CD4(+) stage prior to being positively selected. These data suggest that positive selection is not a prerequisite for the differentiation of DP thymocytes into TSP CD4(+) thymocytes. We propose a model in which positive selection and differentiation into the TSP CD4(+) stage are separable events and Gads is only required for positive selection.
Analysis of the Retrograde Transport of Glial Cell Line-Derived Neurotrophic Factor (GDNF), Neurturin, and Persephin Suggests That<i>In Vivo</i>Signaling for the GDNF Family is GFRα Coreceptor-Specific (1999)

Neurturin (NRTN) and glial cell line-derived neurotrophic factor (GDNF) are members of a family of trophic factors with similar actions in vitro on certain neuronal classes. Retrograde transport of GDNF and NRTN was compared in peripheral sensory, sympathetic, and motor neurons to determine whether in vivo these factors are transported selectively by different neuronal populations. After sciatic nerve injections, NRTN was transported by sensory neurons of the dorsal root ganglion (DRG). Competition studies demonstrated only limited cross-competition between NRTN and GDNF, indicating selective receptor-mediated transport of these factors. By using immunohistochemistry, we identified two populations of NRTN-transporting DRG neurons: a major population of small, RET-positive, IB4-positive, non-TrkA-expressing neurons that also show the ability to transport GDNF and a minor population of calretinin-expressing neurons that fail to transport GDNF. Spinal motor neurons in the adult showed relatively less ability to transport NRTN than to transport GDNF, although NRTN prevented the cell death of neonatal motor neurons in a manner very similar to GDNF (Yan et al., 1995) and persephin (PSPN) (Milbrandt et al., 1998). Last, NRTN, like GDNF, was not transported to sympathetic neurons of the adult superior cervical ganglion (SCG) after injection into the anterior eye chamber. These data reveal a high degree of functional selectivity of GDNF family receptor-alpha (GFRalpha) coreceptor subtypes for NRTN and GDNF in vivo.
Visual traversability analysis for micro planetary rover (2009)

Traversability analysis is a significant and challenging problem for planetary rover's navigation and safeguard on rocky and bumpy terrain. Moreover, the growing requirement for the micro rover in future planetary missions demands robust traversability analysis upon limited sensors and field of perception. In this paper, a framework for stereo based terrain mapping and traversability analysis in autonomous navigation is developed for the micro planetary rover. In this work, a joint reliability based disparity expansion (JRDE) algorithm is proposed to obtain accurate 3D information of the local terrain. Focusing on the low complexity and robust performance, we report a hierachical digital elevation map (DEM) based method to achieve the traversability map with relative index value, which consists of elevation thresholding and estimation of slope and roughness. Path planning is subsequently fulfilled upon the traversability map. This method is validated with a set of planet-surface like scenes, while complete onboard system has also been proved fast and effective in artificial rocky environment.
Effect of Particle Size of Different Crop Starches and Their Flours on Pasting Properties (2011)

The effect of particle size reduction on the pasting properties of rice, wheat, corn (maize), potato, sweet potato, and cassava starches was elucidated. Before pulverizing, the mean particle size and the pasting properties of the starches differed by crop. With increased pulverizing, the mean particle size decreased in all flours (to＜10μm) and the pasting properties converged. Commercial flours containing the larger starch granules have the higher starch damage after pulverization.
2017 포항지진에 의한 필로티형 내력벽건물의 구조손상 분석 (2019)

In 2017 Pohang Earthquake, a number of residential buildings with pilotis at their first level were severely damaged. In this study, the results of an analytical investigation on the seismic performance and structural damage of two bearing wall buildings with pilotis are presented. The vibration mode and lateral force-resisting mechanism of the buildings with vertical and plan irregularity were investigated through elastic analysis. Then, based on the investigations, methods of nonlinear modeling for walls and columns at the piloti level were proposed. By performing nonlinear static and dynamic analyses, structural damages of the walls and columns at the piloti level under 2017 Pohang Earthquake were predicted. The results show that the area and arrangement of walls in the piloti level significantly affected the seismic safety of the buildings. Initially, the lateral resistance of the piloti story was dominated mainly by the walls resisting in-plane shear. After shear cracking and yielding of the walls, the columns showing double-curvature flexural behavior contributed significantly to the residual strength and ductility.
Preservice Teachers’ Views: Issues for Learning to Teach SOSE in an Overcrowded Curriculum (2013)

A cohort of third-year preservice teachers (n=24) was given the opportunity to observe and participate in Studies of Society and Environment (SOSE) in primary classrooms through a series of school visits during a semester-long unit. These visits were designed to give preservice teachers opportunities to connect SOSE teaching theories studied in the university setting to SOSE teaching practices within schools. This study investigates the extent of the preservice teachers’ opportunities to observe SOSE teaching in the primary school. Responses from a survey showed that the majority of preservice teachers only agreed with 6 of the 25 items associated with the six categories (personal-professional skill development, system requirements, teaching practices, student behavior, feedback to students, and reflection on practice). Written responses from the questionnaire concurred that most had not experienced SOSE teaching. Various issues are discussed around providing preservice teachers with SOSE teaching experiences. School executives, teachers and university staff need to be part of the process to ensure preservice teachers are receiving quality SOSE teaching experiences that will assist in their pedagogical development. A wider question is also raised through this paper. If preservice teachers are unable to experience quality SOSE teaching in school visits designed for such a purpose, does this signal a changing emphasis in education that leaves the social sciences and humanities off the education agenda?
The Maintenance of Plasmid-containing Organisms in Populations of Escherichia coli (1981)

Populations of Escherichia coli containing a small non-conjugative plasmid were grown in carbon-limited continuous culture. For all plasmids tested the presence of the plasmid lowered the growth rate of the host bacterium, and the proportion of plasmid-containing organisms in the total population declined initially. However, periodically, adaptive changes occurred in plasmid-containing organisms which increased their growth rate. This resulted in oscillations in the proportion of plasmid-containing organisms, and the delayed loss of the plasmid from the population.
Role of Cys‐603 in dimer/oligomer formation of the breast cancer resistance protein BCRP/ABCG2 (2005)

Breast cancer resistance protein (BCRP/ABCG2) is a half-molecule ATP-binding cassette transporter that we have previously suggested might function as a homodimer, bridged by disulfide bonds. In the present study, we carried out cysteine-scanning mutagenesis, substituting Ser for Cys, and established 12 PA317 transfectants expressing BCRP mutants with possible disruptions to their S-S bonds. Western blot analysis of BCRP from the wild-type transfectants (PA/WT) confirmed that the wild-type protein migrates as a 140-kDa dimer under non-reducing conditions, but as a 70-kDa monomer under reducing conditions. However, under non-reducing conditions the BCRP-C603S mutant migrated both as a 70-kDa monomer and a 140-kDa dimer, whereas all other mutant BCRP migrated only as dimers. PA317 cells transfected with C603S-BCRP (PA/C603S) showed either similar or only marginally lower SN-38 resistance than PA/WT cells, despite the reduced levels of BCRP dimer in these cells. Moreover, the degree of SN-38 resistance in the mutant BCRP transfectants was found to be associated with the monomer expression levels under reducing conditions. Reverse transcription-polymerase chain reaction analysis showed that the BCRP mRNA levels were similar in the transfectants. We subsequently generated six C603X mutants of BCRP (X=D, H, R, Y, A and W) and carried out western blot analysis and drug sensitivity assays. The results were equivalent to those from the PA/C603S cells, with some variations that again corresponded to the monomer levels. Our findings suggest that Cys-603 is an important residue in the covalent bridge between BCRP monomers but that a functioning unit of BCRP may not necessarily require covalent linkages.
Antiglucocorticoid action of dehydroepiandrosterone in young obese Zucker rats. (1992)

Dehydroepiandrosterone (DHEA) reduces weight gain in the hypercorticosteronemic Zucker fatty rat, an animal model of genetic obesity. However, the mechanism of action of DHEA is still unclear. We propose that DHEA acts as an antiglucocorticoid in the Zucker fatty rat. To test this hypothesis we examined DHEA's ability to block the activation of the glucocorticoid-inducible enzymes tyrosine aminotransferase (TAT) and ornithine decarboxylase (ODC) by dexamethasone (i.p. 5 micrograms/100 g body weight) in hepatic tissue of 6-10 week old Zucker rats. Injections of DMSO, the vehicle, served as a control. DHEA alone did not affect TAT, but when DHEA (500 micrograms/100 g b.w.) was administered simultaneously with dexamethasone, activation did not occur. Similar results were seen using a second tissue (kidney). We conclude that DHEA can act acutely as an antiglucocorticoid in the young obese Zucker rat and hypothesize that its chronic anti-obesity effect may reflect, at least in part, a chronic antiglucocorticoid activity.
E-cadherin and, in Its Absence, N-cadherin Promotes Nanog Expression in Mouse Embryonic Stem Cells via STAT3 Phosphorylation (2012)

We have recently shown that loss of E-cadherin in mouse embryonic stem cells (mESCs) results in significant alterations to both the transcriptome and hierarchy of pluripotency-associated signaling pathways. Here, we show that E-cadherin promotes kruppel-like factor 4 (Klf4) and Nanog transcript and protein expression in mESCs via STAT3 phosphorylation and that β-catenin, and its binding region in E-cadherin, is required for this function. To further investigate the role of E-cadherin in leukemia inhibitory factor (LIF)-dependent pluripotency, E-cadherin null (Ecad(-/-)) mESCs were cultured in LIF/bone morphogenetic protein supplemented medium. Under these conditions, Ecad(-/-) mESCs exhibited partial restoration of cell-cell contact and STAT3 phosphorylation and upregulated Klf4, Nanog, and N-cadherin transcripts and protein. Abrogation of N-cadherin using an inhibitory peptide caused loss of phospho STAT3, Klf4, and Nanog in these cells, demonstrating that N-cadherin supports LIF-dependent pluripotency in this context. We therefore identify a novel molecular mechanism linking E- and N-cadherin to the core circuitry of pluripotency in mESCs. This mechanism may explain the recently documented role of E-cadherin in efficient induced pluripotent stem cell reprogramming.
Coating Electrospun Chitosan Nanofibers with Polyelectrolyte Multilayers Using the Polysaccharides Heparin and <i>N</i>,<i>N</i>,<i>N</i>‐Trimethyl Chitosan (2010)

A new method is presented for functionalizing electrospun nanofibers with GAGs and growth factors by PEM deposition. Electrospun chitosan nanofibers, spun from trifluoroacetic acid and dichloromethane, were coated with PEMs, using the polysaccharides heparin and N,N,N-trimethyl chitosan. FGF-2 was adsorbed on the PEM-coated nanofibers. Nanofiber neutralization, PEM construction, and FGF-2 adsorption were monitored using FT-IR spectroscopy and X-ray photoelectron spectroscopy. Alcian blue staining was used to confirm the presence of heparin. SEM was used to study nanofiber morphology.
Debug information validation for optimized code (2020)

Almost all modern production software is compiled with optimization. Debugging optimized code is a desirable functionality. For example, developers usually perform post-mortem debugging on the coredumps produced by software crashes. Designing reliable debugging techniques for optimized code has been well-studied in the past. However, little is known about the correctness of the debug information generated by optimizing compilers when debugging optimized code.