gebhart/patrepeval huggingface dataset:
Linear placement algorithms and applications to VLSI design (1987)

Abstract A linear placement technique that uses an objective function of the sum of wiring lengths is proposed. The method evolves from well‐known concepts in job sequencing and network flow. The relation between a job sequencing problem and this linear placement problem was demonstrated by Lawler. Also, Sidney proposed decomposition algorithms for job sequencing problems. Building on Lawler's and Sidney's work, we first develop a polynomial‐time algorithm to obtain optimal solutions for the special case of parallel graphs. Adolphson and Hu applied the max‐flow min‐cut method of the network flow problem to the partitioning of general placement problems. However, when the cut operation creates the cut of the same configuration as the previous cut operations, no additional partitioning information is obtained. We devise an optimal graph modification that tries to change the configuration of the cut for further partitioning of the problem, and achieve the maximum partitioning of the problem. Finally, a heuristic algorithm is derived to solve some Very Large Scale Integrated Circuits (VLSI) design linear placement problems. A comparison with published papers shows that our VLSI placement method produces better results.
Soil Bacteria Confer Plant Salt Tolerance by Tissue-Specific Regulation of the Sodium Transporter HKT1 (2008)

Elevated sodium (Na(+)) decreases plant growth and, thereby, agricultural productivity. The ion transporter high-affinity K(+) transporter (HKT)1 controls Na(+) import in roots, yet dysfunction or overexpression of HKT1 fails to increase salt tolerance, raising questions as to HKT1's role in regulating Na(+) homeostasis. Here, we report that tissue-specific regulation of HKT1 by the soil bacterium Bacillus subtilis GB03 confers salt tolerance in Arabidopsis thaliana. Under salt stress (100 mM NaCl), GB03 concurrently down- and upregulates HKT1 expression in roots and shoots, respectively, resulting in lower Na(+) accumulation throughout the plant compared with controls. Consistent with HKT1 participation in GB03-induced salt tolerance, GB03 fails to rescue salt-stressed athkt1 mutants from stunted foliar growth and elevated total Na(+) whereas salt-stressed Na(+) export mutants sos3 show GB03-induced salt tolerance with enhanced shoot and root growth as well as reduced total Na(+). These results demonstrate that tissue-specific regulation of HKT1 is critical for managing Na(+) homeostasis in salt-stressed plants, as well as underscore the breadth and sophistication of plant-microbe interactions.
Repression of stress-responsive genes by FIERY2, a novel transcriptional regulator in Arabidopsis (2002)

Low temperature, drought, and high salinity induce the expression of many plant genes. To understand the mechanisms for the transcriptional activation of these genes, we conducted a reporter gene-aided genetic screen in Arabidopsis. Seven allelic mutations in the FIERY2 (FRY2) locus result in significant increases in the expression of stress-responsive genes with the DRE/CRT (drought-responsive/C-repeat) cis element but non-DRE/CRT type stress-responsive genes were less affected. The specific regulation of DRE/CRT class of genes by FRY2 appears to be caused by repression of stress induction of the upstream CBF/DREB transcription factor genes. fry2 mutants show increased tolerance to salt stress and to abscisic acid during seed germination but are more sensitive to freezing damage at the seedling stage. FRY2/CPL1 encodes a novel transcriptional repressor harboring two double-stranded RNA-binding domains and a region homologous to the catalytic domain of RNA polymerase II C-terminal domain phosphatases found in yeast and in animals that regulate gene transcription. These data indicate that FRY2 is an important negative regulator of stress gene transcription and suggest that structured RNA may regulate hormone and stress responses in plants as it does in animals.
IgG2m4, an engineered antibody isotype with reduced Fc function (2009)

The Fc region of an antibody mediates effector functions such as antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC), and plays a key role in the in vivo half-life of an antibody. In designing antibody therapeutics, it is sometimes desirable that the antibody has altered Fc-mediated properties. In the case of a "benign blocker" antibody, it is often desirable to diminish or abolish the ADCC and CDC functions while retaining its PK profile. Here, we report a novel engineered IgG isotype, IgG2m4, with reduced Fc functionality. IgG2m4 is based on the IgG2 isotype with four key amino acid residue changes derived from IgG4 (H268Q, V309L, A330S and P331S). An IgG2m4 antibody has an overall reduction in complement and Fc gamma receptor binding in in vitro binding analyses while maintaining the normal in vivo serum half-life in rhesus.
Genetic Approaches to Electrogenic Proton Transport by a Yeast H+-ATPase (1994)

A genetic approach is used to probe electrogenic proton transport by the Saccharomyces cerevisiae plasma membrane H+-ATPase (PMA1). Mutations in PMA1 , selected by growth resistance to hygromycin B, cause a depolarization of cellular membrane potential. Enzyme from one mutant, pma1-105 (Ser368 → Phe), is largely insensitive to imposed membrane voltage and appears to catalyze electroneutral H+ transport. A countercurrent of K+ may provide charge compensation in this enzyme. Second-site mutations that partially revert the pma1-105 phenotype were identified within the membrane sector and provide strong evidence for coupling between cytoplasmic and membrane domains. Mutations conferring hygromycin B resistance have been identified in both cytoplasmic and membrane domains, and multiple transmembrane segments are presumed to be important for electrogenic H+ transport. However, a special emphasis is placed on the role of transmembrane segments 1 and 2, which provide the starting point for a more inclusive structural model of the membrane sector.
Hybrid Phase Locked Loop for controlling Centralized inverters in large solar Photovoltaic power plants (2016)

This paper presents a hybrid Phased Locked Loop (PLL) algorithm for 500kW-1MW grid-connected Centralized inverters for large Photovoltaic (PV) power plants. Proposed Hybrid PLL with ZCD enables faster synchronization during inverter start-up and can be used in high power master-slave based centralized inverters which are being used in large PV power plant. Three phase PLL structures such as Synchronous Reference Frame (SRF), Double Decoupled SRF (DDSRF), Enhanced PLL (EPLL), Double Second Order General Integral (DSOGI) and DSOGI with Frequency Locked Loop (FLL) are discussed and a comparative analysis of these PLL techniques is done with proposed PLL technique. The proposed PLL technique is simulated in MATLAB/SIMULINK and digitally implemented in TMS320F2812 based Discrete Signal Controller (DSC). The performance of the proposed PLL technique is experimentally validated with unbalanced and distorted grid signals.
V beta 17 T cell receptor peptide vaccination in rheumatoid arthritis: results of phase I dose escalation study. (1996)

Further controlled studies are required to assess the biologic and clinical efficacy of this treatment approach.
DDX3Y encodes a class I MHC–restricted H-Y antigen that is expressed in leukemic stem cells (2008)

The Y chromosome encodes male-specific minor histocompatibility (H-Y) antigens that stimulate T- and B-lymphocyte responses after sex-mismatched allogeneic hematopoietic cell transplantation (HCT). A CD8(+) cytotoxic T lymphocyte (CTL) clone that recognizes a novel HLA-B*2705-restricted H-Y antigen encoded by the DDX3Y gene was isolated from a male who had received a hematopoietic cell graft from his human leukocyte antigen (HLA)-identical sister. The antigenic peptide is a decamer that differs from the homologous DDX3X-encoded peptide at 4 positions. Expression of DDX3Y and of the H-Y epitope that it encodes was examined by quantitative polymerase chain reaction (PCR) and by CTL recognition assays. Expression of DDX3Y is detected in all myeloid and lymphoid leukemic cells that carry an intact Y chromosome. Moreover, the DDX3Y-encoded H-Y epitope is presented on the surface of both myeloid and lymphoid leukemic cells from male HLA-B*2705(+) patients. DDX3Y-specific CTLs prevent engraftment of human acute leukemia in nonobese diabetic/severe combined immune deficient mice, demonstrating that the DDX3Y-encoded H-Y antigen is also expressed in leukemic stem cells. These results demonstrate that CD8(+) T-cell responses against DDX3Y have the potential to contribute to graft-versus-leukemia (GVL) activity after female into male allogeneic HCT. This study is registered at http://clinicaltrials.gov as NCT00107354.
Improvement of palm oil through breeding and biotechnology (1997)

Abstract The oil palm Elaeis guineensis is the highest oil‐yielding crop and has the potential to become the major supplier of both edible oil and renewable industrial feedstock. The oil yield from wild groves is presently less than 0.5 t/ha/y. However, through breeding and selection, the oil yield of commercial plantations could reach as much as 8 t/ha/y. New planting materials also have the capability of better oil yields with high iodine value (IV), slow height increment, and larger kernels. The oil also contains considerable amounts of carotenoids (500–700 ppm), vitamin E (600–1000 ppm), and sterols (250–620 ppm). The oil yield of another oil palm species, E. oleifera , is approximately 0.5 t/ha/y with high contents of carotenoids (700–1500 ppm), vitamin E (700–1500 ppm), and sterols (3500–4000 ppm). The above traits could be improved through breeding and biotechnology. Biotechnological efforts at the Palm Oil Institute of Malaysia are directed toward the production of oil with high IV and high monounsaturated fatty acids for edible purposes and industrial uses. Isolation and manipulation of the genes involved in the biosynthesis of fatty acids are the main focus. The aim is to increase the efficiency of conversion of palmitate (C 16:0 ) to oleate (C 18:1 ). Levels of palmitate and oleate are controlled by the enzymes acyl‐acyl carrier protein (ACP) thioesterase and β‐keto acyl ACP synthase II. The chain termination reactions of C 16:0 and C 18:1 are independent, thus paving the way for the possibility of reducing palmitate levels by switching off the palmitoyl ACP thioesterase gene.
Cloning and expression of Mycobacterium bovis BCG DNA in "Streptomyces lividans" (1986)

The ability of "Streptomyces lividans" to use the expression signals of genes from Mycobacterium bovis BCG was tested in vivo by using gene fusions. Random DNA fragments from M. bovis BCG were inserted into promoter-probe plasmids in Escherichia coli and in "S. lividans." Comparison with promoter activity detected with random DNA fragments from the respective hosts suggested that "S. lividans" efficiently utilizes a high proportion of mycobacterial promoters, whereas a smaller fraction are expressed, and expressed more weakly, in E. coli. M. bovis BCG DNA fragments were also inserted into the specially constructed translational fusion vector (pIJ688) in "S. lividans." pIJ688 contains the kanamycin phosphotransferase gene (neo) from transposon Tn5, truncated at its amino terminus, as the indicator. The results suggested that "S. lividans" uses M. bovis BCG translational signals almost as efficiently as its own signals. Moreover, several hybrid proteins with an M. bovis BCG-derived amino terminus seemed to be reasonably stable in "S. lividans." These experiments indicate that "S. lividans" may be a suitable host for the expression of Mycobacterium leprae and Mycobacterium tuberculosis genes from their own signals. This is a precondition for the expression of entire biosynthetic pathways, which could be valuable in the production of diagnostic and therapeutic agents. The vectors may also have wider applications for the analysis of gene expression in Streptomyces.
Opinosis: A Graph Based Approach to Abstractive Summarization of Highly Redundant Opinions (2010)

We present a novel graph-based summarization framework (Opinosis) that generates concise abstractive summaries of highly redundant opinions. Evaluation results on summarizing user reviews show that Opinosis summaries have better agreement with human summaries compared to the baseline extractive method. The summaries are readable, reasonably well-formed and are informative enough to convey the major opinions. 1
Measurement of the Amplitude and Phase of a Sculpted Rydberg Wave Packet (1998)

We have completely determined the amplitude and phase of a quantum wave packet. The wave packet was shaped using a programmable optical pulse. Phase information comes from analysis of covariant fluctuations due to interference between the wave packet and a well-characterized reference.
A motion compensation technique using sliced blocks in hybrid video coding (2005)

This paper proposes a new motion compensation method using "sliced blocks" in hybrid video coding. In H.264, a brand-new international video coding standard, motion compensation can be performed by splitting macroblocks into multiple square or rectangular regions. In the proposed method, on the other hand, macroblocks or sub-macroblocks are divided into two regions (sliced blocks) by an arbitrary line segment. The result is that the shapes of the segmented regions are not limited to squares or rectangles, allowing the shapes of the segmented regions to better match the boundaries between moving objects. Thus, the proposed method can improve the performance of the motion compensation. In addition, adaptive prediction of the shape according to the region shape of the surrounding macroblocks can reduce overheads to describe shape information in the bitstream. The proposed method also has the advantage that conventional coding techniques such as mode decision using rate-distortion optimization can be utilized, since coding processes such as frequency transform and quantization are performed on a macroblock basis, similar to the conventional coding methods. The proposed method is implemented in an H.264-based P-picture codec and an improvement in bit rate of 5% is confirmed in comparison with H.264.
Management of Diskogenic Pain Using Epidural and Intrathecal Steroids (1977)

The use of methylprednisolone acetate (Depo-Medrol) injected by the epidural or intrathecal route for the relief of diskogenic back pain with or without radiculopathy is an adjunct to conservative management useful when conservative measures fail and surgical treatment is under consideration. This is especially true when symptoms have been present for only a few months. Corticosteroids injected in the same manner seem to have little effect on patients with symptoms persisting for periods longer than 3 months or in patients treated previously by surgical methods.
Equipment review: Cooling catheters to induce therapeutic hypothermia? (2006)

There is growing acceptance within the medical community of induced (therapeutic) hypothermia as a tool to achieve neuroprotection and/or cardioprotection. Although much work remains to be done in identifying those clinical situations in which hypothermia can be effective, there is now sufficient evidence to regard it as a standard of care, at least for some indications such as selected patients with postanoxic encephalopathy. Thus, attention is now partly shifting from assessment of the clinical evidence of efficacy to technical and implementation issues. This review provides a list of criteria by which cooling devices can be judged, and specifically it discusses one of the new cooling devices: the Alsius CoolGard 3000 device and CoolLine catheter. General aspects and advantages/disadvantages of surface versus core cooling are discussed, as are potential side effects, device-specific pros and cons, and cost-effectiveness issues. In addition, the current state of the evidence for use of induced hypothermia for various indications is briefly reviewed.
Cortical neurons express nerve growth factor receptors in advanced age and Alzheimer disease. (1992)

Using a monoclonal antibody directed against the primate nerve growth factor (NGF) receptor, we examined the expression of NGF receptors within neuronal perikarya of normal adult human cerebral cortex (27-98 years old) and individuals with Alzheimer disease (AD). This expression of cortical NGF receptors was compared with that seen in other neurological diseases and normal human development as well as in young and aged nonhuman primates. NGF receptor-containing cortical neurons were not observed in young adults (less than 50 years old) and were observed only infrequently in non-demented elderly individuals (50-80 years old). In contrast, numerous NGF receptor-containing cortical neurons were seen in AD patients of all ages and in one 98-year-old nondemented patient. In advanced age and AD, numerous NGF receptor-positive neurons were located within laminae II-VI of temporal association cortices whereas only a few were seen in the subicular complex, entorhinal cortex, parahippocampal gyrus, and amygdaloid complex. These perikarya appeared healthy, with bipolar, fusiform, or multipolar morphologies and extended varicose dendritic arbors. These neurons failed to express neurofibrillary tangle-bearing material. In contrast to AD, NGF receptor-containing cortical neurons were not observed in Parkinson disease, Pick disease, or Shy-Drager syndrome. The NGF receptor-containing cortical neurons seen in advanced age and AD were similar in morphology to those observed in human fetal cortex. No NGF receptor-containing cortical neurons were observed in young or aged nonhuman primates. These findings suggest that neurons within the human cerebral cortex exhibit plasticity in their expression of NGF receptors in AD and extreme advanced aging.
A first attempt at monitoring underground gas storage by means of time‐lapse multichannel transient electromagnetics (2000)

Two successive transient electromagnetic surveys were carried out over an underground gas storage site in France. The idea was to monitor changes in the gas bubble from the differences in the data. If successful, the new methodology could help to reduce the number of monitoring wells and finally reduce costs. Preliminary 3D modelling indicated that the resistivity changes caused by movements of the gas/water contact should be detectable in the electric field transients provided that the signal‐to‐noise ratio is at least 100:1. The surveys were performed with the TEAMEX multichannel acquisition system, adapted from a seismics system. The highly redundant data were analysed by calculating the relative differences in the electric field transients. The differences were common‐midpoint‐sorted and spatially stacked. Another approach was the calculation of electric field time derivatives in a log–log domain, to eliminate static shift effects which are present in the data. Even though the data quality is excellent from a classical point of view, neither of the two approaches reveals changes in the data which might be caused by changes in the gas reservoir. In future applications to monitoring, transmitters and receivers should be installed permanently, and the transmitter input waveform should be monitored continuously, to avoid some of the problems encountered here. Moreover, the signal‐to‐noise ratio will have to be further increased by at least one order of magnitude.
Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents (2005)

The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of approximately 4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups.
Methane conversion in low-temperature plasma (2009)

The conversion of methane in electric discharges of different types and under electron beam irradiation are considered. The influence of nonequilibrium conditions of conversion in low-temperature plasma on the energy consumption, product composition, and selectivity is analyzed. The results of works on plasma pyrolysis, partial plasma oxidation, and steam and carbon dioxide reforming of methane in a low-temperature plasma are discussed. It is shown that the use of chain processes makes it possible to substantially reduce the power consumption for methane conversion by an electrophysical device.
Functional muscle ischemia in neuronal nitric oxide synthase-deficient skeletal muscle of children with Duchenne muscular dystrophy (2000)

Duchenne muscular dystrophy (DMD) is a fatal disease caused by mutation of the gene encoding the cytoskeletal protein dystrophin. Despite a wealth of recent information about the molecular basis of DMD, effective treatment for this disease does not exist because the mechanism by which dystrophin deficiency produces the clinical phenotype is unknown. In both mouse and human skeletal muscle, dystrophin deficiency results in loss of neuronal nitric oxide synthase, which normally is localized to the sarcolemma as part of the dystrophin-glycoprotein complex. Recent studies in mice suggest that skeletal muscle-derived nitric oxide may play a key role in the regulation of blood flow within exercising skeletal muscle by blunting the vasoconstrictor response to alpha-adrenergic receptor activation. Here we report that this protective mechanism is defective in children with DMD, because the vasoconstrictor response (measured as a decrease in muscle oxygenation) to reflex sympathetic activation was not blunted during exercise of the dystrophic muscles. In contrast, this protective mechanism is intact in healthy children and those with polymyositis or limb-girdle muscular dystrophy, muscle diseases that do not result in loss of neuronal nitric oxide synthase. This clinical investigation suggests that unopposed sympathetic vasoconstriction in exercising human skeletal muscle may constitute a heretofore unappreciated vascular mechanism contributing to the pathogenesis of DMD.