gebhart/patrepeval huggingface dataset:
Improved chemistry for oligodeoxyribonucleotide synthesis substantially improves restriction enzyme cleavage of a synthetic 35mer (1989)

Two DNA duplexes of identical sequence and 35 nt in length were synthesized by an original and a highly improved version of phosphoramidite chemistry. By base composition analysis, DNA synthesized by improved chemistry (termed DMTS-imp) contained no detectable modified bases while DNA synthesized by the original chemistry (termed DMTS-std) had a large number of modifications. Under optimal reaction conditions, HhaI and RsaI cleaved the DMTS-std duplex to 76-77% completion and the DMTS-imp duplex to 96-99% completion. Restriction analysis and piperidine treatment yielded estimates of approximately 3.0% modified nucleotides in DMTS-std and approximately 1.0% in DMTS-imp. Overall, the improvements in chemistry increased the restriction efficiency of synthetic DNA up to 10-fold.
A cyclic somatostatin analog that precipitates withdrawal in morphine-dependent mice. (1987)

We evaluated the ability of the mu selective, peptidic, opioid antagonist CTP to precipitate withdrawal in morphine-dependent mice after intracerebroventricular (i.c.v.) and subcutaneous (s.c.) administration. The withdrawal syndrome evoked by i.c.v. CTP was different in some respects from that observed after i.c.v. naloxone. Naloxone, given i.c.v., produced shakes and tremors, defecation, diarrhea, wet dog shakes, jumping and weight loss. In contrast, the prominent signs following i.c.v. CTP were grooming, tremors and shakes, defecation, wet dog shakes and weight loss. CTP treated mice exhibited a greatly reduced incidence of jumping behaviors and diarrhea. While s.c. naloxone evoked similar effects to i.c.v. naloxone, CTP given s.c. stimulated defecation and modest weight loss only. The differences in the profile of withdrawal signs between naloxone and CTP may be related to their differences in receptor selectivity or possibly to their respective alkaloidal and peptidic natures. The relative lack of behavioral effects seen after s.c. CTP probably reflects the inability of CTP to pass through the blood brain barrier, and indicates that although the majority of withdrawal signs are mediated by centrally located opioid receptors, the gastrointestinal tract can be withdrawn independently of the central nervous system.
Radioligand Binding Characteristics of the Endothelin Receptor in the Rabbit Iris (1998)

We previously suggested the presence of functionally atypical endothelin (ET) A receptors in the rabbit iris sphincter. Here, we further characterized the ET receptor by a radioligand-receptor binding study utilizing a membrane fraction of the rabbit iris. In addition, we functionally confirm the presence of an atypical ET(A) receptor in the iris dilator similar to that in the iris sphincter. In binding experiments, [125I]ET-1 was completely displaced by ET-3 in a biphasic fashion, but only partially by BQ-123 and ET(B) ligands. In the presence of RES-701, ET-3 and sarafotoxin (SRTX)-b completely displaced [125I]ET-1 in a monophasic fashion, but with shallow slopes. Moreover, ET-1, ET-3 and SRTX-b completely displaced [3H]BQ-123 with IC50 values of 0.8, 81 and 4.4 nM, respectively, but with slopes of ET-3 and SRTX-b being again shallow. In iris dilator muscles, ET-3 showed lower and SRTX-b showed higher contractile activities than ET-1. SRTX-c was inactive. BQ-123 more preferentially antagonized ET-3 and SRTX-b than ET-1, with the Schild plot slope of SRTX-b being shallow. Thus, functional experiments suggested the presence of atypical ET(A) receptors in the iris dilator similar to the iris sphincter. However, the binding experiments suggested the presence of rather typical ET(A)- and ET(B)-like receptors. Therefore, we apparently failed to show ET binding sites corresponding to functionally atypical ET(A) receptors.
Broken Railway Fastener Detection Based on Adaboost Algorithm (2010)

The detection of broken railway fastener is important to ensure the safety of the railway transport. This paper proposes an efficient method to detect and recognize the broken fastener with complex ballast railway images. Firstly, a from-coarse-to-fine strategy according to the sleeper region's gray and gradient characteristics is used to position the fastener, then the Haar-like feature set according to the fastener's geometrical characteristics is introduced. Finally, the fastener state is recognized by the AdaBoost-based algorithm. The method can detect fastener effectively and automatically with high positioning and recognizing accuracy and need not manual intervention. The experiment showed that the detection rate is satisfactory.
DIRECT NUMERICAL SIMULATION OF FLOW AND MASS TRANSFER IN SPACER-FILLED CHANNELS (2010)

Thesis (Master, Mechanical and Materials Engineering) -- Queen's University, 2010-11-30 11:44:07.479
Formation of Chlorophenols and Related Compounds in Natural and Technical Chlorination Processes (1991)

Surface water was halogenated by the addition of: (i) chloroperoxidase, hydrogen peroxide and chloride; (ii) hydrogen peroxide and chloride or bromide; (iii) hypochlorite. Analysis of adsorbable organic halogen (AOX), halogenated phenols and purgeable organic compounds showed that reactions (i) and (ii) produced almost the same halogenated compounds. It was also shown that active chlorine occurred as an intermedi-ate in reaction (i). Reaction (ii) implied a marked halogenation only after the addition of bromide, and this reaction was enhanced by a low pH. Existing evidence that 2,4,6-trichlorophenol may be naturally produced was strengthened. Some evidence was also obtained indicating that enzyme-mediated reactions may contribute to the natural formation of dibenzo-p-dioxins.
Client side reconfiguration on software components for load balancing (2002)

The size of applications is becoming greater every day. Software components enable developers to easily build large applications with basic reusable parts. However, there is a need for system support to allow these applications to scale to many users and to large networks. Current methods for load balancing cannot be applied, since they are mostly designed for local area networks and the monitoring tools are not sufficient. To allow efficient load balancing, we first have to consider the architecture of the monitoring infrastructure. In this paper, we present a way to build a scalable monitoring platform. By using information provided by this platform, it's possible to build policies for helping system administrators in the management of complex tasks. Using application descriptions, these policies take into account the global architecture and drive reconfigurations using the monitoring data.
Well-Ordered Nanostructure SiC Ceramic Derived from Self-Assembly of Polycarbosilane-Block-Poly(methyl methacrylate) Diblock Copolymer (2008)

The fabrication of SiC ceramic materials with an ordered nanostructure through the direct pyrolysis of a self-assembled inorganic-organic block copolymer has generally been unsuccessful even though the versatile processibility has been demonstrated with organic-organic block copolymers. Here we report the synthesis of a novel polycarbosilane-block-poly(methyl methacrylate) diblock copolymer through ring-opening living anionic polymerization in a THF and n-hexane solvent system at -48 degrees C. The resulting block copolymer exhibited phase-separation behavior on the nanoscale to form a self-assembled nanostructure that was converted to a mesoporous ceramic after heating at 800 degrees C. The characterization of diblock copolymer is simultaneously investigated by GPC, and NMR analyses. The self-assembly of diblock copolymer is characterized by small-angle X-ray scattering (SAXS), atomic force microscopy (AFM), and scanning electron microscopy (SEM). In particular, the preparation of high-temperature-stable nanostructured silicon carbide and mesoporous silicon carbide ceramic directed from cross-linked polycarbosilane blocks with a high ceramic yield are described, which exhibits well-oriented nanostructures with the size in a range of 4-10 nm. These exciting results have a great potential to open a new field for the generation of nanostructured non-oxide ceramic or metal-ceramic materials for a broad class of applications.
Data from Identification of Loss of p16 Expression and Upregulation of MDR-1 as Genetic Events Resulting from Two Novel Chromosomal Translocations Found in a Plasmablastic Lymphoma of the Uterus (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To establish cell lines from the patient with plasmablastic lymphoma, who was immunologically competent including negative human immunodeficiency virus (HIV) serology, and analyze the unique chromosomal translocations seen in the cell lines in order to unveil the pathogenesis of this tumor, which had no evidence of Epstein-Barr virus involvement.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Establishment of the cell lines was attempted by inoculating the patient's lymph node biopsy specimen subcutaneously to immunodeficient mice. Comparative genomic hybridization (CGH) array and FISH analysis were performed to identify breakpoints of the two chromosomal translocations. Of the 4 candidate genes identified by FISH analysis to be involved in the translocations, reverse transcription-PCR, Western blot, flow cytometry, and proliferation assay were performed to identify the exact genes involved.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Analysis of the cell lines identified loss of p16 at the protein level by chromosomal translocation of t(9;13) and upregulation of MDR-1 by t(4;7). The cell lines expressing MDR-1 acquired resistance to chemotherapeutic agents such as cisplatin and doxorubicin, but not bortezomib. Expression of B lymphoid lineage marker genes of these cell lines was negative for paired box 5 (&lt;i&gt;Pax5&lt;/i&gt;) or PR domain containing 1, with ZNF domain (&lt;i&gt;PRDM1&lt;/i&gt;), but was positive for X-box binding protein 1 (&lt;i&gt;Xbp1&lt;/i&gt;).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We established three novel cell lines of plasmablastic lymphoma. Characterization of the unique chromosomal translocation identified loss of p16 and upregulation of MDR-1 at protein level. Expression of &lt;i&gt;Xbp1&lt;/i&gt;(s), which is involved in the maturation of plasma cells, corresponded to the plasmablastic appearance of the tumor. These cell lines may be a useful tool to understand the pathophysiology of the disease and to develop novel treatment strategies. &lt;i&gt;Clin Cancer Res; 17(8); 2101–9. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Spinal intramedullary cysticercosis of the conus medullaris. (2008)

Neurocysticercosis is the most common central nervous system (CNS) parasitic disease worldwide, but spinal cysticercal infection is relatively rare, especially in the United States. Because of increased immigration to the United States from endemic areas, the incidence of neurocysticercosis has risen, especially in California, Texas, Arizona, and other southwestern states, but not in Wisconsin. Spinal intramedullary cysticercosis involving the conus medullaris is an uncommon clinical condition that can lead to irreversible neurological deficits if untreated. Rarely, Taenia solium, a cestode that causes neurocysticercosis, may produce spinal intramedullary lesion, which may mimic an intramedullary tumor. We report a case of thoracolumbar spinal intramedullary cysticercosis caused by Taenia solium. Spinal neurocysticercosis should be kept in mind in the differential diagnosis of intramedullary conus lesions even if the patient lives in Wisconsin.
Orthopaedic surgery in the palliation of cancer (2015)

Abstract Metastatic spread of cancer to bone is frequent and causes pain, disability, and functional limitation. New understanding of the homing method of cancer cells to bone and the mechanism of cancer production of pain raise possible new treatment strategies. Non-surgical treatments such as chemotherapy and hormone therapy are effective in early disease. Bisphosphonates and inhibition of osteoprotegerin prevent progression of bone lesions and avoid pain, radiation, and surgery. Radiotherapy arrests disease and relieves pain in many cases. Surgery is needed when the bone is weak or fractured. It effectively relieves pain and preserves function. It usually requires replacing or bypassing the deficient bone with site-specific reconstructive surgery. Surgery should be selected based on projections of patient survival. New tools to make these projections have been validated and are now available. New targeted drug therapies appear to be changing metastatic bone disease into a more chronic condition. This will alter the management of local disease in many histological subtypes of metastatic cancers.
Rule compilation from constraint-based problem solving (2002)

A constraint-based system for automating the acquisition of problem-solving knowledge is described. The approach is novel in attempting to compile rules from the observation of constraint-based, relaxation-based problem solving. The system has three main components; a constraint-based problem solver, a rule-compiler and a rule-base problem solver. A relation consistency algorithm is the backbone of the constraint-based problem solver. One advantage of this method is that customized expert systems can be built by manipulating the problems used for learning. Experiments were performed to evaluate a prototype learning system and some extensions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Adaptive transversal filters with delayed coefficient adaptation (2005)

In practical applications of the LMS adaptive transversal filtering algorithm, a delay in the coefficient update is sometimes required. In this paper, the behavior of the Delayed LMS (DLMS) algorithm is studied. A stablility bound for the step size is derived. The relation between the step size and the convergence speed and the effect of the delay on the convergence behavior are also investigated. Computer simulation results are provided and compared with the analytical results.
Pregnancy and neonatal outcome following an antenatal diagnosis of cleft lip and palate (2012)

In cases of CL(P), there is a high incidence of associated anomalies detected on antenatal ultrasound and these significantly increase the risk of poor neonatal outcome.
Three-Dimensional Atomic Structure of Metastable Nanoclusters in Doped Semiconductors (2011)

Aberration-corrected scanning transmission electron microscopy is used to determine the atomic structure of nanoclusters of cerium dopant atoms embedded in silicon. By channeling electrons along two crystallographic orientations, we identify a characteristic zinc-blende chemical ordering within CeSi clusters coherent with the silicon host matrix. Strain energy limits the size of these ordered arrangements to just above 1 nm. With the local order identified, we then determine the atomic configuration of an individual subnanometer cluster by quantifying the scattering intensity under weak channeling condition in terms of the number of atoms. Analysis based on single-atom visualization also evidences the presence of split-vacancy impurity complexes, which supports the hypothesis of a vacancy-assisted formation of these metastable CeSi nanophases.
On Pareto-Koopmans Efficiency for Performance-Driven Optimisation in Self-Organising Networks (2013)

In this paper, a novel Multi-Objective Optimisation (MOO) method has been introduced for Self-Organising Networks (SONs). Meta-heuristic algorithms based on Simulated Annealing (SA) are used to evaluate the Pareto Frontier (PF) of UE throughput vs. fairness index in a simulation of Coverage & Capacity Optimisation (CCO) use-case in SONLTE. We have evaluated the performance optimisation methods through the final optimal set of solutions. The boundaries of the optimal sets are evaluated as PF and compared with the results of the conventional method of Multi-Objective Simulated Annealing (MOSA). We have detected a Pareto improvement for the estimated PF of the proposed method, which outperforms that of MOSA.
Side Channel Analysis Resistant Design Flow (2006)

The threat of side-channel attacks (SCA) is of crucial importance when designing systems with cryptographic hardware or software. The FP6-funded project SCARD enhances the typical micro-chip design flow in order to provide a means for designing side-channel resistant circuits and systems. Appropriate SCA-simulation tools and SCA analysis for the designer of secure systems are part of the project goals. We consider these enhancements for traditional design flows of micro-chips as necessary in order to enable the design for the next generation of secure and dependable devices. SCARD is in its final phase, the final result a SCARD chip designed by using the developed design flow is currently implemented
Cover Feature: The Self‐Assembly of AgI‐Containing Heterobimetallic Complexes with a Discriminatory N,P‐Based Heteroditopic Ligand (Eur. J. Inorg. Chem. 44/2018) (2018)

The Cover Feature shows the unusual heterobimetallic dimeric complexes that are produced when our heteroditopic ligand is reacted with AgI, AgI/ZnII, or AgI/PbII ions. Trying to use self-assembly to form heterobimetallic complexes with AgI can sometimes be a gamble due to its promiscuous nature. However, the high discriminatory power of our ligand's pyrimidine-hydrazone and phosphole based coordination pockets enables the reliable and efficient synthesis of these diverse complexes in one pot reactions. More information can be found in the Full Paper by D. J. Hutchinson and E. Hey-Hawkins.
Using Surface Segregation To Design Stable Ru‐Ir Oxides for the Oxygen Evolution Reaction in Acidic Environments (2014)

Abstract The methods used to improve catalytic activity are well‐established, however elucidating the factors that simultaneously control activity and stability is still lacking, especially for oxygen evolution reaction (OER) catalysts. Here, by studying fundamental links between the activity and stability of well‐characterized monometallic and bimetallic oxides, we found that there is generally an inverse relationship between activity and stability. To overcome this limitation, we developed a new synthesis strategy that is based on tuning the near‐surface composition of Ru and Ir elements by surface segregation, thereby resulting in the formation of a nanosegregated domain that balances the stability and activity of surface atoms. We demonstrate that a Ru 0.5 Ir 0.5 alloy synthesized by using this method exhibits four‐times higher stability than the best Ru‐Ir oxygen evolution reaction materials, while still preserving the same activity.
Genomic landscape of advanced prostate cancer in racial minority populations: Real-world experience in a safety-net hospital oncology clinic. (2021)

14 Background: The largest US cancer health disparity exists in prostate cancer (PC), with African American (AA) men having: ~1.6-1.8-fold higher risk of developing PC; younger age and more advanced stage at diagnosis; increased risk of recurrence after radical prostatectomy; and up to 2.5-fold higher mortality rate relative to men of other ancestries. Access to healthcare and other socioeconomic and environmental factors contribute to the disparity in clinical outcomes. However, genetic factors may also be involved, and their role and prevalence need to be better defined, especially in real-world clinical settings, as the high cost of next-generation sequencing (NGS) may have resulted in underrepresentation of uninsured and minority patients in prior studies. Methods: We retrospectively analyzed NGS data obtained via Tempus|xT tissue assay (DNA sequencing of 648 genes in tumor and matched normal samples at 500x depth) and/or Tempus|xF liquid biopsy assay (ctDNA sequencing of 105 genes in peripheral blood samples at 5,000x depth) for germline and/or somatic mutations detected in 100 patients (53 AA) receiving androgen deprivation therapy for locally advanced, biochemically recurrent or metastatic PC at Ben Taub Hospital (BTH), a safety net hospital in Harris County/Houston serving a patient population of which 91% are racial/ethnic minorities. For confirmation, we analyzed de-identified NGS data from a nationwide cohort of 1,211 metastatic PC patients (213 AA) previously sequenced with xT and/or xF by Tempus Labs (Chicago, IL). Results: We found higher frequencies of AR (18.9%), TP53 (41.5%), SPOP (20.7%) and homologous recombination repair (HRR) pathway gene mutations, in particular BRCA2 (17%), in our AA BTH cohort, as compared to PC patients of other races/ethnicities. The latter finding was confirmed in the nationwide Tempus Labs cohort, with 91/213 (42.7%) AA patients exhibiting mutation in at least one of 14 HRR pathway genes associated with PC sensitivity to PARP inhibitors, compared to 347/998 (34.7%) non-AA patients (P &lt; 0.05). This difference was mainly driven by higher frequency of BRCA2 (16.9%), CDK12 (8%) and PALB2 (5.2%) mutations in AA patients. In both cohorts, TMPRSS2 fusions were much less common in AA PC patients. Conclusions: The observed high frequency of mutations in key PC drivers in AA patients may reflect differences in disease biology between racial/ethnic groups or the more advanced disease presentation of AA patients due to socioeconomic factors delaying access to healthcare. Our study provides a real-world snapshot of the genomic landscape of advanced PC in a safety net hospital serving large racial/ethnic minority populations and highlights the role that NGS testing can play to improve their access to treatment with novel targeted therapies and to biomarker-based Precision Oncology clinical trials.
Isolation and characterization of chitinase genes from pitchers of the carnivorous plant Nepenthes khasiana (2006)

The genus Nepenthes represents carnivorous plants with pitcher traps capable of efficient prey capture and digestion. The possible involvement of plant chitinases in this process was studied in Nepenthes khasiana. Two different types of endochitinases were identified in the liquid of closed traps exhibiting substrate specificity for either long chitin polymers or N-acetylglucosamine (GlcNAc) oligomers. Injection of chitin into such closed sterile pitchers induced the appearance of additional endochitinase isoenzymes, with substrate specificity only for long chitin polymers. No significant exochitinase (N-acetyl-beta-glucosaminidase) or chitobiosidase activity could be detected in the non-induced or induced trap liquid. Four genes representing two subgroups of basic chitinases, denoted as Nkchit1b and Nkchit2b, were isolated from the secretory region of N. khasiana pitchers. The main differences between the two subgroups are the presence of a proline-rich hinge region only in NkCHIT1b and a C-terminal putative vacuole targeting extension only in NkCHIT2b, indicating different compartmentalization of the two enzymes. Reverse transcription-polymerase chain reaction (RT-PCR) evaluation of mRNA levels showed that the Nkchit2b genes are constitutively expressed in the secretory cells while transcription of Nkchit1b genes is induced by chitin injection. These results show for the first time the involvement of genes encoding chitinases in prey-trap interaction and their differential expression and activity during prey trapping.