gebhart/patrepeval huggingface dataset:
Genetic and biochemical characterization of dTOR, the Drosophila homolog of the target of rapamycin (2000)

The adaptation of growth in response to nutritional changes is essential for the proper development of all organisms. Here we describe the identification of the Drosophila homolog of the target of rapamycin (TOR), a candidate effector for nutritional sensing. Genetic and biochemical analyses indicate that dTOR impinges on the insulin signaling pathway by autonomously affecting growth through modulating the activity of dS6K. However, in contrast to other components in the insulin signaling pathway, partial loss of dTOR function preferentially reduces growth of the endoreplicating tissues. These results are consistent with dTOR residing on a parallel amino acid sensing pathway.
Experiences implementing a high performance TCP in user-space (1995)

The advantages of user-space protocols are well-known, but implementations often exhibit poor performance. This paper describes a user-space TCP implementation that outperforms a 'normal' kernel TCP and that achieves 80% of the performance of a 'single-copy' TCP. Throughput of 160 Mbit/s has been measured. We describe some of the techniques we used and some of the problems we encountered.
Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides (2012)

The longitudinal evolution of a myeloma genome from diagnosis to plasma cell leukemia has not previously been reported. We used whole-genome sequencing (WGS) on 4 purified tumor samples and patient germline DNA drawn over a 5-year period in a t(4;14) multiple myeloma patient. Tumor samples were acquired at diagnosis, first relapse, second relapse, and end-stage secondary plasma cell leukemia (sPCL). In addition to the t(4;14), all tumor time points also shared 10 common single-nucleotide variants (SNVs) on WGS comprising shared initiating events. Interestingly, we observed genomic sequence variants that waxed and waned with time in progressive tumors, suggesting the presence of multiple independent, yet related, clones at diagnosis that rose and fell in dominance. Five newly acquired SNVs, including truncating mutations of RB1 and ZKSCAN3, were observed only in the final sPCL sample suggesting leukemic transformation events. This longitudinal WGS characterization of the natural history of a high-risk myeloma patient demonstrated tumor heterogeneity at diagnosis with shifting dominance of tumor clones over time and has also identified potential mutations contributing to myelomagenesis as well as transformation from myeloma to overt extramedullary disease such as sPCL.
Cells and Extracellular Matrices of Dentin and Pulp: A Biological Basis for Repair and Tissue Engineering (2004)

Odontoblasts produce most of the extracellular matrix (ECM) components found in dentin and implicated in dentin mineralization. Major differences in the pulp ECM explain why pulp is normally a non-mineralized tissue. In vitro or in vivo, some dentin ECM molecules act as crystal nucleators and contribute to crystal growth, whereas others are mineralization inhibitors. After treatment of caries lesions of moderate progression, odontoblasts and cells from the sub-odontoblastic Höhl's layer are implicated in the formation of reactionary dentin. Healing of deeper lesions in contact with the pulp results in the formation of reparative dentin by pulp cells. The response to direct pulp-capping with materials such as calcium hydroxide is the formation of a dentinal bridge, resulting from the recruitment and proliferation of undifferentiated cells, which may be either stem cells or dedifferentiated and transdifferentiated mature cells. Once differentiated, the cells synthesize a matrix that undergoes mineralization. Animal models have been used to test the capacity of potentially bioactive molecules to promote pulp repair following their implantation into the pulp. ECM molecules induce either the formation of dentinal bridges or large areas of mineralization in the coronal pulp. They may also stimulate the total closure of the pulp in the root canal. In conclusion, some molecules found in dentin extracellular matrix may have potential in dental therapy as bioactive agents for pulp repair or tissue engineering.
The progression of cognitive impairment in dementia with Lewy bodies, vascular dementia and Alzheimer's disease (2001)

Over 1 year, DLB, VaD and AD patients had similar rates of cognitive decline overall. Apolipoprotein E4 may be an important predictor of more rapid decline in DLB.
Anticoagulation and Antiplatelet Therapy in Dermatology (2009)

An increasing number of patients who are receiving anticoagulation or antiplatelet therapy require cutaneous surgery. Such pharmacotherapies are usually suspended based on experience in gynecologic, thoracic, and abdominal surgery. However, this practice may increase the risk of suffering a thromboembolic event. We review perioperative management of anticoagulant and antiplatelet therapy, complications associated with suspending therapy, and side effects.
A novel endothelial-specific membrane protein is a marker of cell-cell contacts. (1992)

mAbs were raised in mice against cultured human endothelial cells (EC) and screened by indirect immunofluorescence for their ability to stain intercellular contacts. One mAb denoted 7B4 was identified which, out of many cultured cell types, specifically decorated cultured human EC. The antigen recognized by mAb 7B4 is bound at the appositional surfaces of cultured EC only as they become confluent and is stably expressed at intercellular boundaries of confluent monolayers. EC recognition specificity was maintained when the antibody was assayed by immuno-histochemistry in tissue sections of many normal and malignant tissues and in blood vessels of different size and type. The antigen recognized by 7B4 was enriched at EC intercellular boundaries similarly in vitro and in situ. In vitro, addition of mAb 7B4 to confluent EC increased permeation of macromolecules across monolayers even without any obvious changes of cell morphology. In addition, when EC permeability was increased by agents such as thrombin, elastase, and TNF/gamma IFN, its distribution pattern at intercellular contact rims was severely altered. mAb 7B4 immunoprecipitated a major protein of 140 kD from metabolically and surface-labeled cultured EC extracts which appeared to be an integral membrane glycoprotein. On the basis of its distribution in cultured cells and in tissues in situ, 7B4 antigen is distinct from other described EC proteins enriched at intercellular contacts. NH2-terminal sequencing of the antigen, immunopurified from human placenta, and sequencing of peptides from tryptic peptide maps revealed identity to the cDNA deduced sequence of a recently identified new member of the cadherin family (Suzuki, S., K. Sano, and H. Tanihara. 1991. Cell Regul. 2:261-270.) These data indicate that 7B4 antigen is an endothelial-specific cadherin that plays a role in the organization of lateral endothelial junctions and in the control of permeability properties of vascular endothelium.
Reduction of the renal uptake of radiolabeled monoclonal antibody fragments by cationic amino acids and their derivatives. (1995)

The renal uptake of radiolabeled antibody fragments and peptides is a problem in radioimmunodetection and radioimmunotherapy, especially with intracellular retained radiometals. The aim of this study was to develop suitable methods to reduce this kidney uptake. BALB/c mice or nude mice bearing the human GW-39 colon carcinoma xenograft were given i.p. injections of basic amino acids or a range of different basic amino acid derivatives, amino sugars, as well as cationic peptides. The effect of these agents on the biodistribution of Fab' and F(ab')2 fragments of different mAbs radiolabeled with 99mTc, 188Re, 111In, 88Y, or 125I was studied. Tumor and organ uptake was determined and compared to untreated mice. The kidney uptake of Fab' fragments was reduced 5-6-fold in a dose-dependent manner as compared to untreated controls. The uptake in all other organs, as well as the tumor, was unaffected. A similar reduction in renal retention was seen for all other intracellularly retained isotopes, as well as for F(ab')2 fragments. D- and L-isomers of lysine were equally effective whether given i.p. or p.o. D-glucosamine was effective, but its N-acetyl derivative was not. Basic polypeptides (e.g., poly-L-lysine) were also effective; their potency increased with increasing molecular weight. HPLC of the urine taken from treated animals showed the excretion of intact Fab', in contrast to mostly low-molecular-weight metabolites in the control group. These studies indicate that a variety of basic compounds is capable of inhibiting the tubular reabsorption of peptides and proteins, thus lowering the kidney uptake of antibody fragments significantly. On a molecular basis, the effect seems to essentially rely on the presence of a positively charged amino group. By reducing renal retention of antibody fragments, their role as imaging and therapeutic agents may be expanded.
Apicidin Attenuates MRSA Virulence through Quorum-Sensing Inhibition and Enhanced Host Defense (2019)

Recurrent epidemics of drug-resistant Staphylococcus aureus illustrate the rapid lapse of antibiotic efficacy following clinical implementation. Over the last decade, community-associated methicillin-resistant S. aureus (MRSA) has emerged as a dominant cause of infections, and this problem is amplified by the hyper-virulent nature of these isolates. Herein, we report the discovery of a fungal metabolite, apicidin, as an innovative means to counter both resistance and virulence. Owing to its breadth and specificity as a quorum-sensing inhibitor, apicidin antagonizes all MRSA agr systems in a non-biocidal manner. In skin challenge experiments, the apicidin-mediated abatement of MRSA pathogenesis corresponds with quorum-sensing inhibition at in vivo sites of infection. Additionally, we show that apicidin attenuates MRSA-induced disease by potentiating innate effector responses, particularly through enhanced neutrophil accumulation and function at cutaneous challenge sites. Together, these results indicate that apicidin treatment represents a strategy to limit MRSA virulence and promote host defense.
Expression of Costimulatory Molecules on Human Retinoblastoma Cells Y-79: Functional Expression of CD40 and B7H1 (2006)

These results suggest that CD40 expressed on Y-79 plays an important role in augmenting antitumor immunity. In contrast, the expression of B7H1 on IFN-gamma-treated Y-79 cells contributes to the suppression of T cells. The dual effects of CD40 and B7H1 on Y-79 cells may contribute to positive or negative regulation of antitumor immune responses in human retinoblastoma.
Fundamentals of Plant Genetics and Breeding (1981)

The only introductory text available with a detailed description of Mendelian genetic principles necessary for the understanding and application of plant breeding methods. Organized by principles rather than by crops, allowing the instructor to build the teaching system from simple concepts to complex programs. Covers such topics as: breeding objectives that introduce the student to the concept of program development by objectives rather than by individual crop species; program design and management; and new developments in scientific investigations, including wide genetic transfer and tissue culture. Questions to aid the student in understanding genetic principles are given at the end of several chapters. A glossary of important terms is also included.
Directed Differentiation of Human-Induced Pluripotent Stem Cells Generates Active Motor Neurons (2009)

The potential for directed differentiation of human-induced pluripotent stem (iPS) cells to functional postmitotic neuronal phenotypes is unknown. Following methods shown to be effective at generating motor neurons from human embryonic stem cells (hESCs), we found that once specified to a neural lineage, human iPS cells could be differentiated to form motor neurons with a similar efficiency as hESCs. Human iPS-derived cells appeared to follow a normal developmental progression associated with motor neuron formation and possessed prototypical electrophysiological properties. This is the first demonstration that human iPS-derived cells are able to generate electrically active motor neurons. These findings demonstrate the feasibility of using iPS-derived motor neuron progenitors and motor neurons in regenerative medicine applications and in vitro modeling of motor neuron diseases.
El valor de los escombros: Iniciativas públicas para elevar el porcentaje de residuos constructivos reciclados (2002)

El 90% de los residuos que genera la actividad constructora, denominados RCD, podria recuperarse y reutilizarse como materia prima para la construccion. A traves de programas y planes de gestion especificos, ensayos tecnicos e investigacion de nuevos materiales se han dado los primeros pasos de aproximacion aal objetivo de maximo aprovechamiento de los escombros
Notiz zur Synthese von Alkyl‐, Cycloalkyl‐ und Aryl‐3‐aminophenylsulfonen (1981)

Syntheses of Some Alkyl, Cycloalkyl and Aryl 3‐Aminophenyl Sulfones Syntheses of alkyl ( 1a – 1i, 1m ), cycloalkyl ( 1j, 1k ) and aryl ( 1l ) 3‐aminophenyl sulfones were achieved by ethanolic Béchamp ‐reduction of the appropriate 3‐nitrophenyl sulfones ( 3a – 3m ). The alkyl ( 3a – 3i ) and cycloalkyl ( 3j, 3k ) 3‐nitrophenyl sulfones were prepared via nitration of their respective sulfones ( 2a – 2k ). Methyl (3‐nitrophenyl) sulfone ( 3a ) was also prepared by condensation of 3‐nitrobenzenesulfinic acid ( 4 ) with bromoacetic acid to 3‐nitrophenylsulfonyl‐acetic acid ( 5 ) followed by decarboxylation.
FORMATION OF NATURAL SOILS (2012)

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Copper-Catalyzed Halogen Exchange in Aryl Halides:  An Aromatic Finkelstein Reaction (2002)

A mild and general method for the conversion of aryl, heteroaryl, and vinyl bromides into the corresponding iodides was developed utilizing a catalyst system comprising 5 mol % of CuI and 10 mol % of a 1,2- or 1,3-diamine ligand. A variety of polar functional groups are tolerated, and even N-H containing substrates such as sulfonamides, amides, and indoles are compatible with the reaction conditions. Both the reaction rate and the equilibrium conversion of the aryl bromide depend on the choice of the halide salt and the solvent. The best results were obtained using NaI as the halide salt and dioxane, n-butanol, or n-pentanol as the solvents.
A Decision Tree Framework for Spatiotemporal Sequence Prediction (2015)

We study the problem of learning to predict a spatiotemporal output sequence given an input sequence. In contrast to conventional sequence prediction problems such as part-of-speech tagging (where output sequences are selected using a relatively small set of discrete labels), our goal is to predict sequences that lie within a high-dimensional continuous output space. We present a decision tree framework for learning an accurate non-parametric spatiotemporal sequence predictor. Our approach enjoys several attractive properties, including ease of training, fast performance at test time, and the ability to robustly tolerate corrupted training data using a novel latent variable approach. We evaluate on several datasets, and demonstrate substantial improvements over existing decision tree based sequence learning frameworks such as SEARN and DAgger.
Synthesis and Biochemical Evaluation of Phosphonoformate Oligodeoxyribonucleotides (2006)

Phosphonoformate oligodeoxyribonucleotides were prepared via a solid phase synthesis strategy. The first step in the preparation of appropriate synthons was condensation of bis(N,N-diisopropylamino)phosphine and diphenylmethylsilylethyl chloroformate in the presence of sodium metal to yield formic acid, [bis(N,N-diisopropylamino)phosphino]-beta-(diphenylmethylsilylethyl) ester. The product of this reaction was then condensed with appropriately protected 2'-deoxynucleosides using 4,5-dicyanoimidazole to yield the 3'-O-phosphinoamidite reactive monomers. The exocyclic amines of cytosine, adenine, and guanine were protected with 9-fluorenylmethyloxycarbonyl, and oligodeoxyribonucleotides were synthesized on controlled pore glass using the hydroquinone-O,O'-diacetic acid linker. Synthons were sequentially added to this support using tetrazole as an activator, oxidized to phosphonoformate, and the transient 5'-protecting group was removed with acid. Following total synthesis of an oligomer, protecting groups were removed with TEMED.HF and products purified by HPLC. These analogues were resistant to nucleases, formed duplexes with complementary RNA (A-form), and, as chimeric oligomers containing phosphate at selected sites, stimulated RNase H1 activity.
Arginine, a Key Residue for the Enhancing Ability of an Antifreeze Protein of the Beetle Dendroides canadensis (2009)

Antifreeze proteins (AFPs) can produce a difference between the nonequilibrium freezing point and the melting point, termed thermal hysteresis (TH). The TH activity of an antifreeze protein (AFP) depends on the specific AFP and its concentration as well as the presence of cosolutes including low molecular mass solutes and/or proteins. We recently identified series of carboxylates and polyols as efficient enhancers for an AFP from the beetle Dendroides canadensis. In this study, we chemically modified DAFP-1 using the arginine-specific reagent 1,2-cyclohexanedione. We demonstrated that 1,2-cyclohexanedione specifically modifies one arginine residue and the modified DAFP-1 loses its enhancing ability completely or partially in the presence of previously identified enhancers. The stronger the enhancement ability of the enhancer on the native DAFP-1, the stronger the enhancement effect of the enhancer on the modified DAFP-1. The weaker enhancers (e.g., glycerol) completely lose their enhancement effect on the modified DAFP-1 due to their inability to compete with 1,2-cyclohexanedione for the arginine residue. Regeneration of the arginine residue using hydroxylamine fully restored the enhancing ability of DAFP-1. These studies indicated that an arginine residue is critical for the enhancing ability of DAFP-1 and the guanidinium group of the arginine residue is important for its interaction with the enhancers, where the general mechanism of arginine-ligand interaction is borne. This work may initiate a complete mechanistic study of the enhancement effect in AFPs.
DNA-Templated Synthesis: More Versatile than Expected (2002)

Nucleic acids direct chemical reactions. Recent examples of DNA-templated synthesis suggest that DNA can direct various chemical reactions sequence-specifically and independent of distance in a surprisingly general manner.
Measurement and analysis of IP network usage and behavior (2000)

Traffic, usage, and performance measurements are crucial to the design, operation and control of Internet protocol networks. This article describes a prototype infrastructure for the measurement, storage, and correlation of network data of different types and origins from AT&T's commercial IP network. We focus first on some novel aspects of the measurement infrastructure, then describe analyses that illustrate the power of joining different measured data sets for network planning and design.
Individual Patient-Specific Immunity against High-Grade Glioma after Vaccination with Autologous Tumor Derived Peptides Bound to the 96 KD Chaperone Protein (2012)

These data provide the first evidence in humans of individual patient-specific immune responses against autologous tumor derived peptides bound to HSP-96.
Design and fabrication of organic complementary circuits (2001)

We have used a simple model description of single field effect transistor characteristics to design organic complementary circuits ranging in complexity from simple inverters through 48-stage shift registers and three-bit row decoders. The circuits were fabricated using standard silicon photolithographic techniques to define the metal, insulator, and interconnect levels. The ohmic source and drain contacts and part of the interconnect metallization were formed by electroless/immersion deposition of Ni-P/Au on prepatterned TiN. The n-type and p-type organic semicondcutors were evaporated onto these substrates to complete the circuits. Measured circuit characteristics were in reasonable agreement with simulations based on the simple device model.
Human hybridomas constructed with antigen-specific Epstein-Barr virus-transformed cell lines. (1982)

A 6-thioguanine-resistant, human lymphoblastoid B-cell line (GM1500 6TG A-11; IgG secreting) was mutagen-treated with low-level gamma-irradiation and selected for ouabain resistance. One line showing 10,000-fold higher drug resistance, designated KR-4, was fused with an Epstein-Barr virus-transformed, cloned, B-lymphocyte cell line (B6) producing antitetanus toxoid (TT) antibody (IgM), and the hybrids were selected in hypoxanthine/aminopterin/thymidine medium containing 10 microM ouabain. Surviving cells, which arose at an optimal frequency of 10(-5), were subcloned by limiting dilution and screened for anti-TT production. Out of 395 final subclones, 372 were found positive for anti-TT, and seven that were selected for further study secreted specific antibody (IgM, kappa chain) at a maximum concentration of 3-6 micrograms/ml. The differential rate of anti-TT production during the logarithmic phase of cell growth was 15-fold higher in the hybridomas than in the original B6 line. The hybrid nature of the clones was confirmed by karyotype analysis, histocompatibility antigen typing, and expression of secreted and membrane-bound Ig classes. Biosynthetic labeling of the cells revealed that all hybrids secreted both IgM and IgG but that only the IgM class had specificity for TT. Because Epstein-Barr virus is a polyclonal B-lymphocyte activator, the technique we applied here may be useful for increasing the recovery of rare antigen-specific B cells in the peripheral blood and for improving the frequency and stability of hybridomas secreting a given antibody.
ChemInform Abstract: A Novel Convenient One‐Pot Synthesis of N‐Mono‐ and N,N‐Di‐Substituted Thioamides Mediated by 1‐Trifluoromethylsulfonylbenzotriazole. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Diurnal Cortisol Changes in Newborn Infants Suggesting Entrainment of Peripheral Circadian Clockin Uteroand at Birth (2012)

In the newborn infant, diurnal increase in cortisol was observed in the late afternoon and in correspondence with the birth time. The adrenal circadian rhythm acquired in utero may be reentrained by endocrinological events at birth. Such complex regulation of the adrenal circadian clock may inhibit a swift synchronization of the circadian clock to the day-night rhythm.
N-Methylamino Acids in Peptide Synthesis. II. A New Synthesis of N-Benzyloxycarbonyl, N-Methylamino Acids (1973)

Reaction of N-benzyloxycarbonyl derivatives of aliphatic amino acids, and threonine, aspartic, and glutamic acids whose side-chains were protected with the t-butyl group, gave the corresponding N-methylamino acid derivatives in good yields. The methionine derivative could be obtained by using only one mol of methyl iodide. Derivatives of threonine, and aspartic and glutamic acids whose side-chains were not protected could not be methylated. Analysis of the crude products of methylation in three cases showed that they contained 0–1% of racemized material.