gebhart/patrepeval huggingface dataset:
Water-Soluble Dendrigrafts Bearing Saccharidic Moieties:  Elaboration and Application to Enzyme Linked OligoSorbent Assay (ELOSA) Diagnostic Tests (2005)

The synthesis of a series of water-soluble galactopyranose-functionalized polystyrene-polyvinyl ether dendrigrafts and their characterization (in solution and thin solid deposits) have been achieved. The presence of external galactopyranose groups on dendritic polymers has been exploited to prepare dendrigraft-oligonucleotide conjugates using a simple one-step coupling procedure with amino-ended oligonucleotides (ODNs). Several parameters such as the peripherical density of hydrophilic branches, the polymerization degree of polystyrene or poly(hydroxyethyl vinyl ether) blocks, and the number of galactopyranose groups were tuned. A capture test with short labeled complementary ODNs (25 bases) confirmed the presence of covalently bound ODNs on various kinds of dendrigrafts. The ability of the dendritic polymers to enhance the sensitivity of enzyme-linked oligosorbent assay (ELOSA) diagnostic tests (detection of hepatitis B virus, DNA target of 2400 bases) was then evaluated, especially the influence of the macromolecular architecture and the impact of the structural parameters. The dendrigraft-ODN conjugate with the lower saccharide external density was found to lead to a very significant amplification of the fluorescence signal, corresponding to a limit of sensitivity of 10(9) DNA copies per milliliter (instead of 10(11) DNA copies per milliliter without using dendrigrafts). Conversely, the dendrigrafts exhibiting a very high number of branches and galactopyranose groups at their periphery were not able to induce a better sensitivity due to steric hindrance generated by the peripheral congestion on these polymers.
Bendable n‐Type Metallic Nanocomposites with Large Thermoelectric Power Factor (2016)

Highly bendable n-type thermoelectric nanocomposites are successfully developed by embedding metallic Ni nanowires within an insulating poly(vinylidene fluoride) (PVDF) matrix in solution. These nanocomposites exhibit an abnormal decoupling of the electrical conductivity and Seebeck coefficient as a function of Ni contents. A maximum power factor of 220 µW m<sup>-1</sup> K<sup>-2</sup> and ZT of 0.15 can thus be obtained with 80 wt% Ni at 380 K.
Incorporation of a Doubly Functionalized Synthetic Amino Acid into Proteins for Creating Chemical and Light-Induced Conjugates (2015)

Z-Lysine (ZLys) is a lysine derivative with a benzyloxycarbonyl group linked to the ε-nitrogen. It has been genetically encoded with the UAG stop codon, using the pair of an engineered variant of pyrrolysyl-tRNA synthetase (PylRS) and tRNA(Pyl). In the present study, we designed a novel Z-lysine derivative (AmAzZLys), which is doubly functionalized with amino and azido substituents at the meta positions of the benzyl moiety, and demonstrated its applicability for creating protein conjugates. AmAzZLys was incorporated into proteins in Escherichia coli, by using the ZLys-specific PylRS variant. AmAzZLys was then site-specifically incorporated into a camelid single-domain antibody specific to the epidermal growth factor receptor (EGFR). A one-pot reaction demonstrated that the phenyl amine and azide were efficiently linked to the 5 kDa polyethylene glycol and a fluorescent probe, respectively, through specific bio-orthogonal chemistry. The antibody was then tested for the ability to form a photo-cross-link between its phenylazide moiety and the antigen, while the amino group on the same ring was used for chemical labeling. When incorporated at a selected position in the antibody and exposed to 365 nm light, AmAzZLys formed a covalent bond with the EGFR ectodomain, with the phenylamine moiety labeled fluorescently prior to the reaction. The present results illuminated the versatility of the ZLys scaffold, which can accommodate multiple reactive groups useful for protein conjugation.
Can Turned Inward Patella Predict an Excess of Femoral Anteversion During Gait in Spastic Diplegic Children? (2013)

Level IV.
shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data (2021)

Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community, we built an easy-to-use browser, shinyDepMap (https://labsyspharm.shinyapps.io/depmap). shinyDepMap combines CRISPR and shRNA data to determine, for each gene, the growth reduction caused by knockout/knockdown and the selectivity of this effect across cell lines. The tool also clusters genes with similar dependencies, revealing functional relationships. shinyDepMap can be used to (1) predict the efficacy and selectivity of drugs targeting particular genes; (2) identify maximally sensitive cell lines for testing a drug; (3) target hop, that is, navigate from an undruggable protein with the desired selectivity profile, such as an activated oncogene, to more druggable targets with a similar profile; and (4) identify novel pathways driving cancer cell growth and survival.
Hematopoietic Stem Cells in Neural-crest Derived Bone Marrow (2016)

Hematopoietic stem cells (HSCs) in the endosteum of mesoderm-derived appendicular bones have been extensively studied. Neural crest-derived bones differ from appendicular bones in developmental origin, mode of bone formation and pathological bone resorption. Whether neural crest-derived bones harbor HSCs is elusive. Here, we discovered HSC-like cells in postnatal murine mandible, and benchmarked them with donor-matched, mesoderm-derived femur/tibia HSCs, including clonogenic assay and long-term culture. Mandibular CD34 negative, LSK cells proliferated similarly to appendicular HSCs, and differentiated into all hematopoietic lineages. Mandibular HSCs showed a consistent deficiency in lymphoid differentiation, including significantly fewer CD229 + fractions, PreProB, ProB, PreB and B220 + slgM cells. Remarkably, mandibular HSCs reconstituted irradiated hematopoietic bone marrow in vivo, just as appendicular HSCs. Genomic profiling of osteoblasts from mandibular and femur/tibia bone marrow revealed deficiencies in several HSC niche regulators among mandibular osteoblasts including Cxcl12. Neural crest derived bone harbors HSCs that function similarly to appendicular HSCs but are deficient in the lymphoid lineage. Thus, lymphoid deficiency of mandibular HSCs may be accounted by putative niche regulating genes. HSCs in craniofacial bones have functional implications in homeostasis, osteoclastogenesis, immune functions, tumor metastasis and infections such as osteonecrosis of the jaw.
Adverse Food Reactions (1995)

Adverse food reaction is the broad descriptive term given to clinically abnormal responses that occur after the ingestion of food or food additives. These responses can be divided into those that do not involve the immune system (food intolerance) and those that are mediated by the immune system (food allergy or hypersensitivity). There are many causes of food intolerance, including the presence of toxic contaminants such as histamine in scombroid fish; the pharmacologic properties of the food, as with tyramine in cheese; a metabolic dysfunction in the patient, such as lactase deficiency; and idiosyncratic responses. The term food allergy is used to describe responses mediated by the host immune system, independent of any physiologic effect of the food or food additive.
Chlorination of Hydrogenated Silicon Nanosheets Revealed by Solid-State Nuclear Magnetic Resonance Spectroscopy (2023)

Two-dimensional silicon nanosheets (Si-NS) synthesized by topotactic deintercalation of CaSi2 are hypothesized to consist of buckled layers of sp3-hybridized silicon atoms that are bonded to three other framework Si atoms and a terminal atom or functional group such as H, Cl, or OH. Here, we apply 1H{35Cl} and 29Si{35Cl} Resonance-Echo Saturation-Pulse DOuble-Resonance (RESPDOR) solid-state NMR experiments to directly confirm the presence of chlorinated Si atoms within Si-NS. Plotting the 1H{35Cl} RESPDOR dephasing as a function of the 35Cl saturation pulse offset reveals that the 35Cl quadrupolar coupling constant (CQ) is 38 MHz, consistent with Cl atoms that are covalently bonded to silicon. Modeling the 1H{35Cl} RESPDOR dephasing curve shows that the Si–Si interlayer spacing is approximately 6 Å. Plane-wave density functional theory (DFT) calculations show that the direct band gap transition of the Si-NS decreases with increasing chlorination and hydroxylation, suggesting that the band gap of Si-NS can be tuned by modifying the terminal atoms or functional groups.
Towards Haskell in the cloud (2011)

We present Cloud Haskell, a domain-specific language for developing programs for a distributed computing environment. Implemented as a shallow embedding in Haskell, it provides a message-passing communication model, inspired by Erlang, without introducing incompatibility with Haskell's established shared-memory concurrency. A key contribution is a method for serializing function closures for transmission across the network. Cloud Haskell has been implemented; we present example code and some preliminary performance measurements.
Supplementary Figure S1 from AZD4573 Is a Highly Selective CDK9 Inhibitor That Suppresses MCL-1 and Induces Apoptosis in Hematologic Cancer Cells (2023)

&lt;p&gt;Identification of highly selective and potent CDK9 inhibitor, AZD4573.&lt;/p&gt;
Quantum Simulation of Many-Body Hamiltonians Using Perturbation Theory with Bounded-Strength Interactions (2008)

We show how to map a given $n$-qubit target Hamiltonian with bounded-strength $k$-body interactions onto a simulator Hamiltonian with two-body interactions, such that the ground-state energy of the target and the simulator Hamiltonians are the same up to an extensive error $O(ϵn)$ for arbitrary small $ϵ$. The strength of the interactions in the simulator Hamiltonian depends on $ϵ$ and $k$ but does not depend on $n$. We accomplish this reduction using a new way of deriving an effective low-energy Hamiltonian which relies on the Schrieffer-Wolff transformation of many-body physics.
A single administration of Fc-fused recombinant human IL-7 induces expansions of T lymphocytes in healthy adults and cancer patients (2020)

Abstract Interleukin-7 (IL-7) is a cytokine that plays important roles in T cell development and homeostasis. IL-7 is a potent agent for promoting T cell reconstruction in lymphopenia patients. In this study, we investigated the effects of GX-I7 (human IL-7 fused to hyFcTM for half-life extension and improved stability) in healthy volunteers (20~60 μg/kg, n=24) and advanced solid cancer patients who had no available effective treatments (60~1,200 μg/kg, n=33). We observed significant increases in the number of circulating CD8+ and CD4+ T cells in healthy volunteers, the peak of which was seen on days 14-21. Importantly, naïve, TEM, and TCM subsets of CD8+ and CD4+ T cells increased, coupled with upregulation of Ki-67. TCR diversity of the naïve T cells tends to be increased in healthy adults by single administration of GX-I7. In addition, cytokine secretion assay using PBMCs revealed that Ag–specific (CMV-specific) T cell responses were maintained after GX-I7 administration in healthy volunteers. Moreover, in advanced solid cancer patients, GX-I7 administration significantly increased the number of all subsets (naïve, TEM, TCM and TEMRA) of both CD8+ and CD4+ T cells in a dose-dependent manner. More importantly, single GX-I7 administration increased the absolute lymphocyte count above the normal range in all patients with lymphopenic conditions (ALC &amp;lt; 1,000/mm3). In conclusion, following GX-I7 administration, dose-dependent increase of ALC and T cell subsets were observed. Our study suggests that GX-I7 as a T cell amplifier provides a unique opportunity for immuno-oncology combination strategies by reconstituting persistent T cell immunity, where anti-tumor effects are mediated by T cells.
Abstract 139: MicroRNA-375 and microRNA-221: Potential noncoding RNAs associated with antiproliferative activity of benzyl isothiocyanate in pancreatic cancer (2011)

Abstract Large high-throughput studies in patients with pancreatic cancer revealed that oncogenic miR-221 is commonly upregulated microRNA whereas putative tumor suppressor miR-375 is generally down modulated when compared to adjacent benign pancreatic tissue or normal pancreas. In our laboratory, we observed that deregulated expression of miR-375 and miR-221 (as noted in pancreatic cancer patients) can be recapitulated in PDX1-Cre+; KRasG12D+ pancreatic cancer mouse model. Coherent data obtained from pancreatic cancer patient samples to preneoplastic lesions developed in preclinical mouse model tempted us to postulate that aberrant expression of these miRNAs (−375 and-221) might play significant role for the development of pancreatic cancer. Interestingly, ablation of miR-221 by ectopic expression of antagomir-221 in pancreatic ductal carcinoma cells can significantly exert antiproliferative effect with increased expression of p27kip1, a target of miR-221. To the other end, premiR-375 overexpression diminished cell proliferation with downmodulation of Insulin like growth factor binding protein 5 (IGFBP5) and Caveolin-1 (CAV-1 gene), which are of particular interest because of their potential link with pancreatic cancer cell growth and diagnosis. It is quite intriguing that the levels of both CAV-1 and IGFBP5 expression were elevated when miR-375 expression wanes in KRASG12D driven PanIN lesion in compound mutant mice. Previous studies in our laboratory demonstrate that benzyl isothiocyanate (BITC), a prototypical member of the isothiocyanate (ITC) family, inhibits proliferation of human pancreatic cancer cells by causing cell cycle arrest and inducing apoptosis. Interestingly, real time qRT-PCR analysis indicates that anticancer agent BITC can diminish oncogenic miR-221 expression and elevate the level of tumor suppressor miR-375 in pancreatic cancer cells. Besides, genetic manipulation studies revealed that enforced silencing of miR-221 or overexpression of miR-375 enhances the antiproliferative effect of BITC in pancreatic ductal carcinoma cells. Next we explored the efficacy of BITC to interfere with the development of mouse PanIN lesions. Results indicate that pancreata of BITC administered compound mutant mice exhibit reduced level of IGFBP5 protein. Histopathological analysis of the extent of PanINs as well as studies on the magnitude of expression of miR-221/miR-375 and other molecular mediators in these pancreata are in progress. Explicitly, our investigation might provide new insight into nonconventional microRNA replacement therapy against pancreatic cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 139. doi:10.1158/1538-7445.AM2011-139
Energy-Secure System Architectures (ESSA): A Workshop Report (2019)

The Energy-Secure System Architectures (ESSA) workshop series was launched in the beginning of 2011 [in conjunction with the International Symposium on Computer Architecture (ISCA)]. This workshop series was interrupted for a few years, before being resurrected recently in conjunction with the Hardware Security-Focused Conference (HOST 2019). The key new feature of ESSA 2019 was to bring circuit-level power-management experts within the ESSA community to explore a cross-layer approach to energy-secure processor design. We provide a summary description of ESSA 2019 (held on 9-10 May at Tysons Corner, VA, USA).
Side Wall Roughness Reduction in Deep Silicon Oxide Etching Using C2F6 Based ECR-RIBE (1995)

A process using multilayered mask, consisting of either novolak based resist or special type of light insensitive polymer and thin metal, is developed for improving the side wall smoothness of silicon oxide etching. Different techniques are used to reduce the side wall roughness of the mask prior to the underlying silicon oxide etching. The mask smoothness is reduced down to 25 nm using underlying thin metal layer which not only increases the adhesion of the upper resist/polymer with the silicon oxide, but also acts as the etch stopper during patterning of the upper resist/polymer. The side wall smoothness of underlying silicon oxide etching using the smooth polymer mask, is improved down to 60 nm which is better than conventional process where metal mask is used.
Thermal Phase Evolution of Pt−Si Intermetallic Thin Films Prepared by the Activated Adsorption of SiH4on Pt(100) and Comparison to Known Structural Models (1999)

We have investigated the growth, morphology, and phase evolution of Pt−Si intermetallic thin films using scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and Auger electron spectroscopy (AES). These materials were formed through an “inverted” CVD deposition process that involves the exposure of a Pt(100) crystal to silane (SiH4) followed by flash annealing treatments. Structural studies performed as a function of the annealing temperature reveal a complicated phase behavior that involves the sequential formation of four atomically ordered phases with multilevel character. The nature of this process is analyzed to obtain information about the primary structure-determining interactions responsible for the phase transformations seen in this system. We describe the structure-determining influences seen on the Pt(100) surface and provide a comparison with earlier results obtained on Pt(111) and Ni surfaces. The substrate effects are marked and the differences between the results obtained on Pt(100) and Pt(111) are discussed in detail. A model is presented that relates the structure of the phases obtained on the Pt(100) surface to known bulk Pt silicide phases. Of particular interest is the finding that “inverted” CVD via the thermolytic decomposition of SiH4 on the Pt(100) substrate yields, upon suitable thermal treatment, a (√17×√17)R14.0° overlayer structure exhibiting two chiral surface domains. This multilayer structure is well described by a termination of the bulk Pt−Si intermetallic phase that is isomorphic with the well-known Ni12P5 structure.
Experiments on the protection of the thioether in methionine (1982)

The decrease in the solubility of peptides when their methionine residues are replaced by methionine sulfoxides prompted the exploration of an alternative approach to the protection of the thioether in methionine side chains. Alkylation of tert.-butyloxycarbonyl methionine p-nitrophenyl ester with methyl p-toluenesulfonate yielded the crystalline derivative of methionine S-methyl p-toluenesulfonate which could be incorporated into peptide chains. Alternatively, methionine S-methyl p-toluenesulfonate (Mmt) residues could be generated by the action of methyl p-toulensulfonate on methionine containing peptides. The protecting group remained intact under the conditions of aminolysis and ammonolysis commonly used in peptide synthesis, and it was unchanged after the removal of other blocking groups with trifluoroacetic acid or diethylamine. On treatment with hydrobromic acid in acetic acid the toluenesulfonate anion was replaced by bromide ion, while hydrogenation resulted in the decomposition of the modified methionine side chain. In the process of deprotection Mmt residues could be smoothly converted to methionine residues by thiolysis. Thus, the protecting group functioned well in several respects but an increase in solubility (in dimethylformamide) on alkylation was observed only in a part of the peptide derivatives tested. Therefore, the value of the new approach for the protection of the methionine side chain in peptide synthesis remains to be established.
Future Directions in Mucormycosis Research (2012)

Mucormycosis has emerged as an important opportunistic infection, especially in severely immunosuppressed hosts. The evolving epidemiology, immunopathogenesis, molecular virulence studies, early diagnosis, and pitfalls in designing clinical studies of mucormycosis are discussed in this article.
Robust sound speed estimation for ultrasound-based hepatic steatosis assessment (2017)

Hepatic steatosis is a common condition, the prevalence of which is increasing along with non-alcoholic fatty liver disease (NAFLD). Currently, the most accurate noninvasive imaging method for diagnosing and quantifying hepatic steatosis is MRI, which estimates the proton-density fat fraction (PDFF) as a measure of fractional fat content. However, MRI suffers several limitations including cost, contra-indications and poor availability. Although conventional ultrasound is widely used by radiologists for hepatic steatosis assessment, it remains qualitative and operator dependent. Interestingly, the speed of sound within soft tissues is known to vary slightly from muscle (1.575 mm · µs<sup>-1</sup>) to fat (1.450 mm · µs<sup>-1</sup>). Building upon this fact, steatosis could affect liver sound speed when the fat content increases. The main objectives of this study are to propose a robust method for sound speed estimation (SSE) locally in the liver and to assess its accuracy for steatosis detection and staging. This technique was first validated on two phantoms and SSE was assessed with a precision of 0.006 and 0.003 mm · µs<sup>-1</sup> respectively for the two phantoms. Then a preliminary clinical trial (N = 17 patients) was performed. SSE results was found to be highly correlated with MRI proton density fat fraction (R <sup>2</sup> = 0.69) and biopsy (AUROC = 0.952) results. This new method based on the assessment of spatio-temporal properties of the local speckle noise for SSE provides an efficient way to diagnose and stage hepatic steatosis.
Whole Genome Sequencing to Resolve the Genomic Architecture of Cerebral Palsy in a Canadian Cohort (P13-9.003) (2023)

To capture the full extent of genomic contributions to cerebral palsy (CP) in an unselected cohort.
Wetting Micro- and Nanofluidic Devices Using Supercritical Water (2006)

We describe a method for wetting micro- and nanofluidic devices with water or any other pure liquid. The process is performed by enclosing the fluidic device in a liquid-filled cell, heating the cell to a temperature above the critical point of the liquid, and subsequent cooling of the cell to room temperature. Because the process liquid is essentially a gas during wetting, arbitrary shapes can be wetted. We demonstrate wetting of micro- and nanostructures in a fused-silica device with only a single inlet. The process is low-cost, fast, safe, and very reliable.
Failure recovery in all-optical ULH networks (2006)

After many years of research and industry efforts, ultra long haul (ULH) technologies for DWDM transport are maturing, and carriers are deploying such technology for high capacity and capital savings. Unlike opaque optical networks, how best to recover an all-optical ULH network after failure is still uncertain. This paper analyzes four recovery schemes in this area ranging from restoration speed and restoration cost. Our results suggest that the proposed hot-standby scheme would benefit from both fast restoration and cost efficiency comparing to other schemes.
Application of pattern recognition techniques to the identification of aerospace acoustic sources (1988)

A pattern recognition system was developed that successfully recognizes simulated spectra of five different types of transportation noise sources. The system generates hyperplanes during a training stage to separate the classes and correctly classify unknown patterns in classification mode. A feature selector in the system reduces a large number of features to a smaller optimal set, maximizing performance and minimizing computation.