gebhart/patrepeval huggingface dataset:
Fractal Synthesis (2019)

This paper will describe Fractal Synthesis, which is a new set of synthesis, clustering, and packing algorithms for FPGA devices, which dramatically increases the utilization and effective performance for arithmetic rich designs. The emergence of AI inferencing as a significant new FPGA application has brought some of the shortcomings of the FPGA and current design flows into focus. We describe new results where near 100% logic utilization of the FPGA is not only possible, but deterministic, with consistent high clock rates. Alternately, smaller datapaths can be synthesized, and combined to make chip filling designs. In one benchmark consisting of purely arithmetic datapath for a large Stratix®10 FPGA (E-2 speedgrade), we will show 92% logic utilization at 460 MHz for an automatically placed arithmetic datapath, and 410MHz with 97% logic utilization. Furthermore, we describe new results, where these performance and density level can be applied to non-arithmetic designs, by extending these techniques to placement.
RECTIFICATION OF DIGITAL IMAGERY (1992)

Different methods can be applied to generate digital orthophotos. Three commonly used approaches are analyzed and compared in this paper. They can be applied to rectify both digitized aerial photographs and satellite scenes. These methods are polynomial, projective, and differential rectifications. The first two are defined by analytical transformations between image and orthophoto without considering the geometry and orientation of the camera. They are approximate solutions. The last one models the physical reality of the imaging process by means of the collinearity equations and corrects for relief displacements. All three methods were implemented on a workstation and were tested with digitized aerial photographs and video images. By overlaying GIS data over the digital orthophoto, the quality of the rectification is checked. To determine the planimetric accuracy of the results, the coordinates of targets were measured in a digital orthophoto and compared to known map coordinates.
Selectins: initiators of leucocyte adhesion and signalling at the vascular wall (2015)

The selectins are transmembrane, Ca(2+)-dependent lectins that mediate leucocyte rolling on vascular surfaces, the first adhesive step during inflammation and immune surveillance. Leucocytes express L-selectin, activated platelets express P-selectin, and activated endothelial cells express E- and P-selectin. Rolling involves force-regulated, rapidly reversible interactions of selectins with a limited number of glycosylated cell surface ligands. Rolling permits leucocytes to interact with immobilized chemokines that convert β2 integrins to high-affinity conformations, which mediate arrest, post-arrest adhesion strengthening, and transendothelial migration. However, rolling leucocytes also transduce signals through selectin ligands, the focus of this review. These signals include serial activation of kinases and recruitment of adaptors that convert integrins to intermediate-affinity conformations, which decrease rolling velocities. In vitro, selectin signalling enables myeloid cells to respond to suboptimal levels of chemokines and other agonists. This cooperative signalling triggers effector responses such as degranulation, superoxide production, chemokine synthesis, and release of procoagulant/proinflammatory microparticles. In vivo, selectin-mediated adhesion and signalling likely contributes to atherosclerosis, arterial and deep vein thrombosis, ischaemia-reperfusion injury, and other cardiovascular diseases.
High‐frequency unilateral thalamic stimulation in the treatment of essential and parkinsonian tremor (1997)

Pharmacologic treatment for essential tremor and the tremor of Parkinson's disease is often inadequate. Stereotaxic surgery, such as thalamotomy, can effectively reduce tremors. We performed a multicenter trial of unilateral high-frequency stimulation of the ventral intermedius nucleus of the thalamus in 29 patients with essential tremor and 24 patients with Parkinson's disease, using a blinded assessment at 3 months after surgery to compare clinical rating of tremor with stimulation ON with stimulation OFF and baseline and a 1-year follow-up. Six patients were not implanted because of lack of intraoperative tremor suppression (2 patients), hemorrhage (2 patients), withdrawal of consent (1 patient), and persistent microthalamotomy effect (1 patient). A significant reduction in both essential and parkinsonian tremor occurred contralaterally with stimulation. Patients reported a significant reduction in disability. Measures of function were significantly improved in patients with essential tremor. Complications related to surgery in implanted patients were few. Stimulation was commonly associated with transient paresthesias. Other adverse effects were mild and well tolerated. Efficacy was not reduced at 1 year. Chronic high-frequency stimulation is safe and highly effective in ameliorating essential and parkinsonian tremor.
Expression of HLA-DR antigens by colonic epithelium in inflammatory bowel disease. (1983)

The expression of HLA-DR and HLA-A,B,C antigens by human colonic epithelium has been examined in tissue sections of patients with inflammatory bowel disease using an immunohistological technique. Colonic epithelial cells from all 21 control subjects with histologically normal colonic mucosa were HLA-DR-. In contrast, in nine of 13 patients with active ulcerative colitis and 11 of 12 with active Crohn's disease the epithelium of involved colonic mucosa was HLA-DR+. HLA-DR antigens were found on the epithelium of only one of six patients with ulcerative colitis in remission and one of three with inactive Crohn's disease. Moreover, these antigens were not present on the epithelium of non-inflamed colonic mucosa in two patients with Crohn's disease in whom adjacent involved mucosa showed strong epithelial reactivity. This difference between patients with active and those with inactive disease is highly significant (P less than 0.005). These findings provide further evidence of the importance of cell-mediated immune mechanisms in the pathogenesis of inflammatory bowel disease.
Target Motifs Affecting Natural Immunity by a Constitutive CRISPR-Cas System in Escherichia coli (2012)

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (cas) genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers) that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM) influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs) that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.
Immunodominant regions within the hepatitis C virus core and putative matrix proteins (1992)

The complete amino acid sequences of hepatitis C virus (HCV) core (residues 1 to 115) and putative matrix (residues 116 to 190) proteins were synthesized as 18-residue-long peptides with an 8-amino-acid overlap. The peptides were assayed with 50 human serum samples with antibodies to HCV (anti-HCV) and 46 serum samples without anti-HCV, as determined by several commercial assays. Immunodominant regions were defined within residues 1 to 18, 11 to 28, 21 to 38, 51 to 68, and 101 to 118. The peptides that covered these regions were recognized by 40 of 50 (80%), 42 of 50 (84%), 36 of 50 (72%), 34 of 48 (68%), and 36 of 48 (72%) of the anti-HCV positive serum samples, respectively. Two anti-HCV negative serum samples were each repeatedly reactive with one peptide, but both were found to be negative by confirmatory anti-HCV assays. Four serum samples that were confirmed to be positive for anti-HCV in commercial assays did not recognize any of the peptides that cover the HCV core-matrix regions. Ninety-two percent of anti-HCV-positive serum samples reacted with a combination of peptides covering residues 1 to 18 and 11 to 28. Testing of peptides that contain the reported genotypic variations of the HCV core within the regions at residues 1 to 18, 51 to 68, and 101 to 118 showed that a change from Thr-110 to Asn-110 decreased the reactivities of eight serum samples. In conclusion, we found that human antibodies to the HCV core-matrix protein(s) are mainly directed to linear determinants and can easily be reproduced by using short synthetic peptides. We also found that such antibodies develop in more than 90% of HCV-infected people.
Towards efficient hierarchical designs by ratio cut partitioning (2003)

A partitioning approach called ratio cut is proposed. The authors demonstrate that the ratio cut algorithm can locate the clustering structures in the circuit. Finding the optimal ratio cut is NP-complete. However, in certain cases the ratio cut can be solved by linear programming techniques via the multicommodity flow problem. They also propose a fast heuristic algorithm running in linear time with respect to the number of pins in the circuit. Experiments show good results in all tested cases, and as much as 70% improvement over the Kernighan-Lin algorithm in terms of the proposed ratio metric.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Incorporation of D-Alanine into Lipoteichoic Acid and Wall Teichoic Acid in Bacillus subtilis (1995)

The Bacillus subtilis dlt operon (D-alanyl-lipoteichoic acid) is responsible for D-alanine esterification of both lipoteichoic acid (LTA) and wall teichoic acid (WTA). The dlt operon contains five genes, dltA-dltE. Insertional inactivation of dltA-dltD results in complete absence of D-alanine from both LTA and WTA. Based on protein sequence similarity with the Lactobacillus casei dlt gene products (Heaton, M. P., and Neuhaus, F. C. (1992) J. Bacteriol. 174, 4707-4717), we propose that dltA encodes the D-alanine-D-alanyl carrier protein ligase (Dcl) and dltC the D-alanyl carrier protein (Dcp). We further hypothesize that the products of dltB and dltD are concerned with the transport of activated D-alanine through the membrane and the final incorporation of D-alanine into LTA. The hydropathy profiles of the dltB and dltD gene products suggest a transmembrane location for the former and an amino-terminal signal peptide for the latter. The incorporation of D-alanine into LTA and WTA did not separate in any of the mutants studied which indicates that either one and the same enzyme is responsible for D-alanine incorporation into both polymers or a separate enzyme, encoded outside the dlt operon, transfers the D-alanyl residues from LTA to WTA (Haas, R., Koch, H.-U., and Fischer, W. (1984) FEMS Microbiol. Lett. 21, 27-31). Inactivation of dltE has no effect on D-alanine ester content of both LTA and WTA, and at present we cannot propose any function for its gene product. Transcription analysis shows that the dlt operon is transcribed from a sigma D-dependent promoter and follows the pattern of transcription of genes belonging to the sigma D regulon. However, the turn off of transcription observed before sporulation starts seems to be dependent on the Spo0A and AbrB sporulation proteins and results in a D-alanine-free purely anionic LTA in the spore membrane. The dlt operon is dispensable for cell growth; its inactivation does not affect cell growth or morphology as described for L. casei.
Individual Differences in Locomotor Activity Are Associated with Levels of Tyrosine Hydroxylase and Neurofilament Proteins in the Ventral Tegmental Area of Sprague-Dawley Rats (1993)

We have demonstrated previously that chronic morphine and cocaine treatments increase levels of tyrosine hydroxylase (TH), and decrease levels of neurofilament (NF) proteins, in the ventral tegmental area (VTA), a major dopaminergic brain reward region, of outbred Sprague-Dawley rats. We have also found inherent differences in levels of these proteins in the VTA of inbred rat strains that differ in their behavioral responses to opiates, cocaine, and other drugs of abuse, with the Lewis rat showing higher levels of TH and lower levels of NFs in the VTA compared to the Fischer 344 rat. Based on recent reports that individual differences in drug responses among outbred Sprague-Dawley rats are highly correlated with the animals' locomotor response to novelty, we determined in the present study whether such within-strain differences in locomotor behavior are also associated with differences in levels of TH and NFs in the VTA. Groups of 42 Sprague-Dawley rats were assessed for locomotor activity in a novel environment. The four animals from each group with the lowest locomotor responses (designated L rats), and the four with the highest locomotor responses (designated H rats), were analyzed for TH and NF immunoreactivity by immunoblotting procedures. It was found that the VTA of L rats exhibited higher levels of TH and lower levels of three major NF proteins, NF-200, NF-160, and NF-68, compared to the VTA of H rats. A tendency for similar L versus H differences in TH and NF levels were observed when groups of rats with the second lowest and second highest locomotor responses were compared; no differences were seen in groups whose locomotor responses were closer to the median. These biochemical differences between H and L rats showed regional specificity, with no significant differences seen in several other regions of brain or spinal cord studied. Differences were also observed between L and H rats in their locomotor responses to acute and repeated cocaine exposure. The possible relationship between the individual differences in TH and NFs and individual differences in locomotor activity and other drug-related behaviors is discussed.
Myofibrillogenesis Regulator 1 Gene Mutations Cause Paroxysmal Dystonic Choreoathetosis (2004)

Although MR-1 gene function is unknown, the precedence of ion channel disturbance in other episodic neurologic disorders suggests that the pathophysiologic features of PDC also involve abnormal ion localization. The discovery that MR-1 mutations underlie PDC provides opportunities to explore this condition's pathophysiologic characteristics and may provide insight into the causes of other paroxysmal neurologic disorders as well as the neurophysiologic mechanisms of alcohol and caffeine, which frequently precipitate PDC attacks.
The interaction of human estrogen receptor with DNA is modulated by receptor-associated proteins. (1994)

To better define the role of accessory protein as mediators of estrogen receptor (ER) function, we have used immuno-, steroid-, and site-specific DNA-affinity chromatography to identify and characterize proteins that associate with ER in extracts from ER-expressing Chinese hamster ovary (CHO-ER) cells. Two associated proteins [70 and 55 kilodaltons (kDa)] were observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis silver stain analysis of all three column eluates. Two additional proteins (45 and 48 kDa) were preferentially retained by the ER-specific DNA affinity column. The 70-kDa protein was subsequently identified by Western blot analysis as a heat shock protein (hsp70). The 55-kDa protein was identified by N-terminal microsequencing as a member of the protein disulfide isomerase family. The 48- and 45-kDa proteins remain unidentified. To determine the possible differential effects of estrogen agonists and antagonists on human (h) ER interaction with these proteins, CHO-ER cells were labeled with [35S]methionine in the presence of estradiol, 4-hydroxytamoxifen (OH-Tam; partial agonist/antagonist), or ICI 182,780 (complete antagonist). None of these ligands altered the pattern of associated proteins when hER complexes were isolated by adsorption to the vitellogenin A2 estrogen response element (ERE). However, when hER was isolated by immunoadsorption, a reduction in the level of associated hsp70 was observed following treatment with estradiol or OH-Tam, compared to no treatment or treatment with ICI 182,780. By gel retardation analysis, maximal interaction of affinity-purified hER with ERE occurred in the presence of all four associated proteins. Removal of the 48- and 45-kDa proteins and/or hsp70 resulted in a decrease in hER/ERE association, which could be restored by the addition of purified hsp70 and/or a mixture of the 48- and 45-kDa proteins. The increased stability of the restored complex was due primarily to an increase in the association rate of hER with ERE. These results suggest that accessory proteins may be required for maximal ER interaction with EREs and that estrogens and estrogen antagonists may promote differential retention of hsp70 in the presence or absence of a specific ERE.
Cyproheptadine displays preclinical activity in myeloma and leukemia (2008)

D-cyclins are regulators of cell division that act in a complex with cyclin-dependent kinases to commit cells to a program of DNA replication. D-cyclins are overexpressed in many tumors, including multiple myeloma and leukemia, and contribute to disease progression and chemoresistance. To better understand the role and impact of D-cyclins in hematologic malignancies, we conducted a high throughput screen for inhibitors of the cyclin D2 promoter and identified the drug cyproheptadine. In myeloma and leukemia cells, cyproheptadine decreased expression of cyclins D1, D2, and D3 and arrested these cells in the G(0)/G(1) phase. After D-cyclin suppression, cyproheptadine induced apoptosis in myeloma and leukemia cell lines and primary patient samples preferentially over normal hematopoietic cells. In mouse models of myeloma and leukemia, cyproheptadine inhibited tumor growth without significant toxicity. Cyproheptadine-induced apoptosis was preceded by activation of the mitochondrial pathway of caspase activation and was independent of the drug's known activity as an H1 histamine and serotonin receptor antagonist. Thus, cyproheptadine represents a lead for a novel therapeutic agent for the treatment of malignancy. Because the drug is well tolerated and already approved in multiple countries for clinical use as an antihistamine and appetite stimulant, it could be moved directly into clinical trials for cancer.
Tolerance testing of passive radio frequency identification tags for solvent, temperature, and pressure conditions encountered in an anatomic pathology or biorepository setting (2010)

In this preliminary study, these RFID tags show a high-degree of tolerance to tested solutions, solvents, temperature, and pressure conditions. However, a measurable failure rate is detectable under some circumstances and redundant identification systems such as barcodes may be required with the deployment of RFID systems. We have delineated testing protocols that may be used as a framework for preliminary assessments of candidate RFID tag tolerance to laboratory conditions.
Molecular analysis of natural leaf senescence in Arabidopsis thaliana (1994)

We have analyzed macromolecular changes that are associated with natural leaf senescence in Arabidopsis thaliana . The loss of chlorophyll that is characteristic of leaf senescence is accompanied by a specific pattern of decline of total RNA and protein levels. We have constructed two cDNA libraries representing mRNAs from Arabidopsis leaves at different senescence stages. Six cDNA clones corresponding to mRNAs that substantially increase in abundance during senescence were isolated. The levels of these mRNAs remain elevated into the late stages of senescence when most of the chlorophyll and protein of the leaf has been degraded. Sis cDNA clones that correspond to mRNAs that exhibit contrasting behavior were also identified: the levels of these mRNAs decrease to undetectable levels during senescence. The changes in the levels of these specific mRNAs during the course of senescence are presented. The results indicate that major changes in gene expression occur in Arabidopsis leaves during the process of senescence.
A Progress Report on the Treatment of 157 Patients with Advanced Cancer Using Lymphokine-Activated Killer Cells and Interleukin-2 or High-Dose Interleukin-2 Alone (1987)

We studied the effects of adoptive immunotherapy with lymphokine-activated killer (LAK) cells plus interleukin-2 or therapy with high-dose interleukin-2 alone in 157 patients with metastatic cancer for whom standard therapy had proved ineffective or no standard effective treatment was available. One hundred eight patients were treated with 127 courses of LAK cells plus interleukin-2, and 49 patients were treated with 53 courses of high-dose interleukin-2 alone. Of 106 evaluable patients receiving LAK cells plus interleukin-2, 8 had complete responses, 15 had partial responses, and 10 had minor responses. The median duration of response was 10 months among those with complete responses and 6 months among those with partial responses; the patient with the longest complete response was still in remission 22 months after treatment. Of 46 evaluable patients treated with high-dose interleukin-2 alone, 1 had a complete response (remission greater than 4 months), 5 had partial responses (2, greater than 3, greater than 5, 7, and greater than 11 months), and 1 had a minor response. Seven of the total of nine complete responses still remain in remission. Hypotension, weight gain, oliguria, and elevation of bilirubin and creatinine levels were common, but these side effects resolved promptly after interleukin-2 administration was stopped. There have been four treatment-related deaths among these 157 patients. This immunotherapeutic approach can result in marked tumor regression in some patients for whom no other effective therapy is available at present. Determining its ultimate role in cancer therapy awaits further attempts to increase the therapeutic efficacy of treatment and decrease its toxicity and complexity.
Algorithms for routing in a linear lightwave network (1991)

Routing algorithms are proposed for setting up calls on a circuit-switched basis in linear lightwave networks (LLN), i.e., networks composed only of linear components, including controllable power combiners and dividers, and possibly linear (non-regenerative) optical amplifiers. The overall problem is decomposed into three subproblems: (1) physical path allocation, (2) checking for violations of the special optical constraints on the allocated physical path, and (3) channel assignment. Only point to point connections are considered. The physical path allocation technique uses the K-shortest path algorithm and tries to minimize the number of sources potentially interfering with each other, as a result of the incoming call. A channel assignment heuristic that tends to spread out calls evenly among the available channels works better than one that tries to maximize channel reuse.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>