gebhart/patrepeval huggingface dataset:
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice (1994)

The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
Disposition and Metabolism of Minaprine in the Rat (1985)

After iv. injection (5 mg/kg) to rats, minaprine is cleared rapidly from plasma with an elimination t 1/2 of 34 min. After the same dose but given orally the drug is rapidly absorbed from the rat gastrointestinal tract. The ratio of the area under the curves (AUC) of the parent drug indicates low bioavailability (5%). Two metabolites of minaprine (M3 and M5) appeared rapidly in rat plasma and far exceed minaprine concentrations. Other known urinary metabolites of the drug were undetectable in rat plasma and brain within the limits of the sensitivity of the method. Minaprine rapidly enters the central nervous system and then distributes almost evenly in various regions beyond the blood/brain barrier. It concentrates in brain tissue reaching concentrations two-three times those in plasma. It metabolites enter the brain less rapidly and their brain AUC never reached 50% of the plasma AUC.
TR3/Nur77 in colon cancer cell apoptosis. (2003)

The orphan nuclear receptor TR3/Nur77 has emerged as a viable candidate in the coordinate regulation of cell proliferation and apoptosis, essential for maintaining normal architecture in rapidly renewing tissues such as the colonic mucosa. TR3 induces apoptosis in a number of cell lineages exposed to proapoptotic stimuli by directly targeting the mitochondria, inducing cytochrome c release. Here we report a distinctly different mechanism of TR3-mediated apoptosis in colon cancer cells. Nucleus-to-cytoplasm translocation of a green fluorescent protein-TR3 construct, but not its direct mitochondrial targeting, was associated with apoptosis induced by the short-chain fatty acid, butyrate. Similar results were observed for the nonsteroidal anti-inflammatory drug, sulindac, and the chemotherapeutic drug, 5-fluorouracil. A mutant TR3 construct lacking DNA-binding ability exerted a potent proapoptotic effect in colon cancer cells that was associated with cytochrome c release, an action dependent upon cytoplasmic localization of the construct, but, again, not its direct mitochondrial targeting. We identified a potential role for BAX recruitment to the mitochondria, secondary to cytoplasmic translocation of TR3, in inducing cytochrome c release and in mediating apoptosis. Therefore, TR3 translocation from the nucleus may initiate the apoptotic cascade in colon cancer cells by stimulating other cytosolic proapoptotic molecules to associate with mitochondria.
Conditional Overexpression of Connective Tissue Growth Factor Disrupts Postnatal Lung Development (2009)

Connective tissue growth factor (CTGF) is a member of an emerging family of immediate-early gene products that coordinates complex biological processes during development, differentiation, and tissue repair. Overexpression of CTGF is associated with mechanical ventilation with high tidal volume and oxygen exposure in newborn lungs. However, the role of CTGF in postnatal lung development and remodeling is not well understood. In the present study, a double-transgenic mouse model was generated with doxycycline-inducible overexpression of CTGF in respiratory epithelial cells. Overexpression of CTGF from Postnatal Days 1-14 resulted in thicker alveolar septa and decreased secondary septal formation. This is correlated with increased myofibroblast differentiation and disorganized elastic fiber deposition in alveolar septa. Overexpression of CTGF also decreased alveolar capillary network formation. There were increased alpha-smooth muscle actin expression and collagen deposition, and dramatic thickening in the peribronchial/peribronchiolar and perivascular regions in the double-transgenic lungs. Furthermore, overexpression of CTGF increased integrin-linked kinase expression, activated its downstream signaling target, Akt, as well as increased mRNA expression of fibronectin. These data demonstrate that overexpression of CTGF disrupts alveologenesis and capillary formation, and induces fibrosis during the critical period of alveolar development. These histologic changes are similar to those observed in lungs of infants with bronchopulmonary dysplasia.
A novel myb‐related gene from Arabidopsis thaliana (1996)

A novel myb-like gene (Atmyb5) has been isolated from a genomic library of Arabidopsis thaliana. The gene contains a single intron in the region coding for the Myb domains. The Myb domains are highly homologous to other animal and plant Myb proteins. Arabidopsis plants transgenic for a chimeric Atmyb5 promoter/GUS gene expressed the enzyme in a developmentally controlled and tissue specific manner. The GUS activity was detected in developing leaf trichomes, stipules, epidermal cells on the margins of young rosette and cauline leaves, and in immature seeds. Atmyb5 mRNA appears between fertilization and the 16 cell stage of embryo development and persists beyond the heart stage.
From visual simulation to virtual reality to games (2005)

During the past decades, the virtual reality community has based its development on a synthesis of earlier work in interactive 3D graphics, user interfaces, and visual simulation. Currently, the VR field is transitioning into work influenced by video games. Because much of the research and development being conducted in the games community parallels the VR community's efforts, it has the potential to affect a greater audience. Given these trends, VR researchers who want their work to remain relevant must realign to focus on game research and development. Leveraging technology from the visual simulation and virtual reality communities, serious games provide a delivery system for organizational video game instruction and training.
Graft copolymerization of methyl methacrylate onto oil palm empty fruit bunch fiber using H2O2/Fe2+ as an initiator (2003)

Abstract Graft copolymerization of methyl methacrylate (MMA) onto oil palm empty fruit bunch fiber (OPEFB) was successfully carried out in aqueous medium using hydrogen peroxide as an initiator. Results from the investigation of the optimum conditions for grafting are presented. Maximum percentage of grafting was achieved when the amount of initiator, cocatalyst, and nitric acid were 5.877 × 10 −3 mol, 2.63 × 10 −4 mol, and 3.24 × 10 −3 mol, respectively. The optimum reaction temperature was 50°C and the reaction period was 120 min. The highest percentage of grafting and grafting efficiency were 220 and 47%, respectively, under optimum conditions. The grafted copolymer was characterized by FTIR spectroscopy and scanning electron microscopy. The presence of a band at 1730 cm −1 provides strong evidence of grafting. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2233–2238, 2003
Imaging Tumors with an Albumin-Binding Fab, a Novel Tumor-Targeting Agent (2007)

Association with albumin as a means to improve biodistribution and tumor deposition of a Fab was investigated using AB.Fab4D5, a bifunctional molecule derived from trastuzumab (HERCEPTIN) capable of binding albumin and tumor antigen HER2 (erbB2) simultaneously. AB.Fab4D5 was compared with trastuzumab and a trastuzumab-derived Fab (Fab4D5) for the ability to target tumors overexpressing HER2 in mouse mammary tumor virus/HER2 allograft models. Biodistribution was monitored using intravital microscopy, histology, and integrated single-photon emission computed tomography/computed tomography analysis. Fab4D5 tumor deposition was characterized by rapid but transient appearance in tumor at 2 h with little retention, followed by rapid accumulation in kidney by 6 h. Trastuzumab was slow to accumulate in tumors and slow to clear from normal tissues, although significant tumor deposition was achieved by 24 h. In contrast, AB.Fab4D5 was observed at 2 h in tumor and its presence was sustained beyond 24 h similar to trastuzumab. Intravital microscopy revealed that at peak tumor accumulation, tumor cell staining by AB.Fab4D5 was more uniform than for Fab4D5 or trastuzumab. Similar tumor deposition was achieved for both AB.Fab4D5 and trastuzumab at 48 h (35.9 +/- 1.8% and 38.2 +/- 3.1% injected dose/g); however, AB.Fab4D5 targeted tumors more rapidly and quickly cleared from blood, leading to a lower overall normal tissue exposure. Importantly, unlike Fab4D5, AB.Fab4D5 did not accumulate in kidney, suggesting that association with albumin leads to an altered route of clearance and metabolism. Rapid targeting, excellent tumor deposition and retention, coupled with high tumor to blood ratios may make AB.Fab an exceptional molecule for imaging and cancer therapy.
Predicting Surgical Outcome Using Bayesian Analysis (1998)

Surgical outcome analysis is best performed using Bayesian statistics. The ability of this type of analysis to take into consideration multiple parameters affecting surgical outcome is a marked improvement over single-condition probabilities that ignore the many degrees of freedom in the dynamics of a surgical intervention. To illustrate the power of a Bayesian analysis a surgical population of 1017 patients undergoing cholecystectomy, colon resection, and appendectomy was developed. Each patient was assigned to a mutually exclusive outcome group (D1, survival; D2, survival with complications; D3, nonsurvival). A priori outcome probabilities for the population were D1 = 0.917, D2 = 0.066, and D3 = 0.017. A conditional probability matrix (CPM) was then developed for 59 patient parameters (Sj) that may have affected outcome. The CPM contained the conditional probability that a parameter was present given the known outcome P(Sj/Di). Once the CPM was matured Bayesian analysis allowed one to predict the surgical outcome given any set or combination of patient parameters P(Di/Sj). Posterior probabilities generated by the Bayes analysis allowed one to investigate the effect of a single parameter or any group of parameters on outcome. Criterion based validity testing based on comparison of Bayesian outcomes versus the surgeons perception of outcomes for computer simulated surgery on 15 artificial patients suggests that this type of analysis provides insightful and educational data to the operating surgeons (V-mortality = 0.547, SEE = 24.46; V-morbidity = 0.319, SEE = 25.86). Objective outcome analysis or surgical peer review cannot be fairly accomplished unless the statistical methodology takes into consideration all of the parameters affecting outcome. This study concludes that Bayes Theorem provides the ideal statistical framework for performing an outcome analysis that considers the many parameters affecting the results of a surgical intervention.
UFBoot2: Improving the Ultrafast Bootstrap Approximation (2017)

The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested data sets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Mapping of the Cystic Fibrosis Locus on Chromosome 7 (1986)

Cystic fibrosis (CF) is the most common autosomal recessive disorder affecting approximately 1 out of 2000 live births in the Caucasian population (Talamo et al. 1983). The major clinical manifestations of CF include chronic obstructive pulmonary disease, pancreatic enzyme insufficiency, and elevated sweat electrolyte levels, all of which are suggestive of an inborn error of metabolism involving exocrine glands. If untreated, CF individuals usually die at an early age due to severe lung infection, but, because of the advances in disease treatment, many patients now survive into adulthood. On the other hand, despite extensive research efforts, the basic defect of this disease remains unknown. Although a defective regulation of chloride ion transport seems to be the most consistent measurable parameter in CF (Knowles et al. 1983; Quinton 1983; Quinton and Bijman 1983; Sato 1984; Widdicombe et al. 1985; Yankaskas et al. 1985), it is still not clear whether this abnormality...
A novel panel of protein biomarkers for predicting response to thalidomide‐based therapy in newly diagnosed multiple myeloma patients (2011)

Multiple myeloma (MM) is a heterogeneous group of disorders both genotypically and phenotypically. Response to thalidomide-based induction therapy in newly diagnosed patients varies significantly in published clinical trials. Proteomic analysis was performed on 39 newly diagnosed MM patients treated with a thalidomide-based regimen (22 responders; 17 non-responders) using immunodepletion, 2-D DIGE analysis and mass spectrometry. Zinc-α-2-glycoprotein (ZAG), vitamin D-binding protein (VDB), serum amyloid-A protein (SAA) and β-2-microglobulin (B2M) had statistically significant higher concentrations in non-responders compared to responders, while haptoglobin (Hp) had a lower concentration. ELISAs were used to validate the candidate protein biomarkers using unfractionated serum from 51 newly diagnosed MM patients (29 responders; 22 non-responders). Using logistic regression, the best possible area under the curve (AUC) was 0.96 using ZAG, VDB and SAA in combination. Leave-one-out-cross-validation (LOOCV) indicated an overall predictive accuracy of 84% with associated sensitivity and specificity values of 81.8 and 86.2%, respectively. Subsequently, 16 of 22 thalidomide-refractory patients successfully achieved complete response or very good partial response using second-line treatment suggesting that the biomarker profile is specific to thalidomide response rather than identifying patients with MM refractory to all therapies. Using a novel panel of predictive biomarkers, the feasibility of predicting response to thalidomide-based therapy in previously untreated MM has been demonstrated.
Atomic force microscope with magnetic force modulation (1994)

We have constructed a scanned stylus atomic force microscope (AFM) with direct force modulation and integrated microfluorescence optics. The instrument was designed to image the surface of massive samples under various ambient conditions. In force modulation microscopy the imaging force is modulated during the scanning process via an external magnetic field that acts directly on the magnetic AFM tip. Polymeric Langmuir–Blodgett films on silicon oxide were imaged to evaluate the application range of the instrument. We demonstrate that direct force modulation microscopy permits the quantitative recording of the local complex compliance both as a function of the location and as a function of the frequency. In a novel imaging mode referred to as sample resonance mode, the contrast of the image can be selectively enhanced based on local elasticity differences.
Lensless On-chip Imaging of Cells Provides a New Tool for High-throughput Cell-Biology and Medical Diagnostics (2009)

Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as approximately 18 cm(2). Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of approximately 5 mm without the need for refocusing which corresponds to up to approximately 9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments.
Cutting Edge: Role of Toll-Like Receptor 9 in CpG DNA-Induced Activation of Human Cells (2001)

Unmethylated CpG motifs present in bacterial DNA stimulate a rapid and robust innate immune response. Human cell lines and PBMC that recognize CpG DNA express membrane-bound human Toll-like receptor 9 (hTLR9). Cells that are not responsive to CpG DNA become responsive when transfected with hTLR9. Expression of hTLR9 dramatically increases uptake of CpG (but not control) DNA into endocytic vesicles. Upon cell stimulation, hTLR9 and CpG DNA are found in the same endocytic vesicles. Cells expressing hTLR9 are stimulated by CpG motifs that are active in primates but not rodents, suggesting that evolutionary divergence between TLR9 molecules underlies species-specific differences in the recognition of bacterial DNA. These findings indicate that hTLR9 plays a critical role in the CpG DNA-mediated activation of human cells.
Induction of apoptosis by bexarotene in cutaneous T-cell lymphoma cells: relevance to mechanism of therapeutic action. (2002)

Bexarotene treatment at clinically relevant concentrations causes apoptosis of CTCL cell lines in association with activation of caspase-3 and cleavage of poly(ADP-Ribose) polymerase, as well as down-regulation of retinoid X receptor alpha, retinoic acid receptor alpha, and survivin. These findings support apoptosis as a mechanism for bexarotene therapy in CTCL.
Characteristics of Bird Community in Mangyeong River Area (2002)

본 연구는 1999년 8월부터 2000년 6월까지 총 4회에 걸쳐 만경강의 조류군집 특성과 관리 방안을 파악하고자 조류군집과 서식환경을 조사하였다. 만경강에서 조류의 서식환경으로 논이 차지하는 비율이 가장 높았으며, 수역, 갯벌, 관목지대, 주거지, 비닐하우스의 순으로 나타났다. 총 88종의 조류가 관찰되었고, 종수는 10월에 58종으로 가장 많았으며, 개체수는 1월에 7,084개체로 가장 많았다. 만경강지역 조류군집의 특성은 잠수성 오리류의 종수가 적고, 상류와 하류의 지역별 서식환경의 차이에 따라 물새의 분포양상이 다르게 나타났다. 수면성 오리류는 삼례대교 상류지역에 주로 분포하였으며, 도요 물떼새류는 하류지역의 갯벌을 주로 이용하였다. 따라서 만경강에 다양한 조류를 서식하게 하기 위해서는 일부 지역에 수심이 1m 이상 되는 지역을 인공적으로 조성하여 잠수성 오리류의 서식을 유도하고, 농경지로 이용되고 있는 하변지역을 관목식생지로 복원할 것을 제안한다. This study was conducted to clarify the characteristics of bird community and habitat types in Mangyeong River area from Aug. 1999 to Jun. 2000. Paddy field was the most dominant land use type. Water area, mudflat, shrub field, urban area and green house were also dominant land use types in study area. Eighty-eight bird species were recorded during study period. Maximum number of species and individuals were shown as 58 species and 7,084 individuals in Oct. and Jan., respectively. There were low number of diving ducks and clumped pattern of waterfowl distribution of bird community in Mangyeong River area. Dabbling ducks distributed at upper reaches near Samrye Bridge, and plovers and sandpipers at lower reaches near estuary. Those results suggest that creation of pools over one meter water-depth and restoration of paddy field into riparian zone with diverse shrubs are required to increase the bird diversity in the Mangyeong rived.
Efficient, Compositional, Order-sensitive n-gram Embeddings (2017)

Adam Poliak, Pushpendre Rastogi, M. Patrick Martin, Benjamin Van Durme. Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics: Volume 2, Short Papers. 2017.
The Homeobox Transcription Factor Prox1 is Absent from the Induced Oval Cells During Rat Liver Regeneration (2005)

Aims: In cases of liver injury, when the hepatocytes' ability to repair the damage, is severely held back, this function might be undertaken by undifferentiated progenitor cells, the so-called oval cells. In vitro, under appropriate conditions, these cells might differentiate into both hepatocytes and bile duct epithelial cells. Prox1, a homeobox transcription factor, takes an important role in embryonic liver development, although it remains expressed in hepatocytes of the adult liver as well; but it is absent from the bile duct epithelial cells. In current study Prox1 expression was examined in the oval cells induced in a rat liver regeneration model. Methods: Prox1 expression was studied at RNA and protein levels in livers of Fisher rats sequentially treated with 2-acetyl-aminofluorene (AAF) combined with partial hepatectomy (PH), and in Wistar rats, treated with CCl4 to induce acute or chronic liver damage. The liver tissues were analysed by immunohistochemical, in situ hybridisation, laser capture and PCR methods. Results: Seven days after PH in AAF treated Fisher rats, typical cell dense areas with oval nuclei were detected and have not shown any Prox1 immunoreaction. Both AAF and CCl4 treatments resulted in decrease of Prox1 expression levels, which was later restored, in addition, the AAF treatment needed a longer restoration period. RNA isolated from laser capture sections of the livers of AAF-treated Fisher rats 7 days after PH has shown Prox1 expression in the central liver parenchyma, and α-fetoprotein in the periportal field. In normal rat liver, in acute and chronic CCl4-induced liver damage and in the rat liver regeneration models: Prox1 was exclusively visible in the nuclei of hepatocytes. Conclusions: Our data demonstrate that besides its importance in embryonic liver development, Prox1 remains expressed in hepatocytes even in case of CCl4-induced liver damage, but is completely absent from cells of the biliary epithelial lineage and from oval cells, induced in rat liver regeneration models. Prox1 does not have a regulation role on hepatocyte specific genes like albumin or α-fetoprotein.