gebhart/patrepeval huggingface dataset:
Queue Register File Optimization Algorithm for QueueCore Processor (2007)

The queue computation model offers an attractive alternative for high-performance embedded computing given its characteristics of short instructions and high instruction level parallelism. A queue-based processor uses a FIFO queue to read and write operands through hardware pointers located at the head and tail of the queue. Queue length is the number of elements stored between the head and the tail pointers during computations. We have found that 95% of the statements in integer applications require a queue length of less than 32 words. The remaining 5% requires larger queue length sizes up to 230 queue words. In this paper we propose a compiler technique to optimize the queue utilization for the hungry statements that require a large amount of queue. We show that for SPEC CINT95 benchmarks, our technique optimizes the queue length without decreasing parallelism. However, our optimization has a penalty of a slight increase in code size.
Transition Metal‐Free N−S Bond Cleavage and C−N Bond Activation of Ugi‐Adducts for Rapid Preparation of Primary Amides and α‐Ketoamides (2023)

A novel method of transition metal-free N-S bond cleavage and subsequent C-N bond activation of Ugi-adducts was developed. Diverse primary amides and α-ketoamides were prepared in a rapid, step-economical and highly efficient manner in two steps. This strategy features excellent chemoselectivity, high yield and functional-group tolerance. Primary amides derived from the pharmaceuticals probenecid and febuxostat were prepared. This method opens a new pathway for the simultaneous synthesis of primary amides and α-ketoamides in an environmentally friendly manner.
Standard autologous tissue flaps for whole breast reconstruction (2020)

Although the use of the latissimus flap has remained stable or decreased in frequency over the past few years, inclusion of the subcutaneous adipose tissue to circumvent the need for an implant has become a popular option, especially in obese patients. If immediate breast reconstruction is being performed, a tissue expander can be placed at the time of the mastectomy under the muscle. If used in skin-sparing mastectomy, a small central skin island is designed and the flap is usually placed directly under the skin. Patients who have tissue expanders placed under the latissimus dorsi flap usually undergo tissue expansion starting at 2 weeks when the incisions are healed. The autologous tissue of the reconstructed breast is a perfect recipient for microdroplet fat grafting, which can often restore skin suppleness and soften the reconstruction following radiotherapy. The markings should be done in a standing position after evaluation of the quantity of tissue which is available for the flap.
Investigating hydrophobic ligand–receptor interactions in parathyroid hormone receptor using peptide probes (2013)

With an increasing number of new chemical entities entering clinical studies, and an increasing share of the market, peptides and peptidomimetics constitute one of the most promising classes of therapeutics. The success of synthetic peptides as therapeutics relies on the lead optimization step in which the lead candidates are modified to improve drug-like properties of peptides related to potency, pharmacokinetics, solubility, and stability, among others. Peptidomimetics based on the N-terminal stretch of the first 11 amino acids of the PTH have been investigated as potential lead compounds for the treatment of osteoporosis. On the basis of a peptide reported in the literature, referred to here as the Parent Peptide (H-Aib-Val-Aib-Glu-Ile-Gln-Leu-Nle-His-Gln-Har-NH2), we conducted systematic SAR analyses to investigate the effects of altering peptide hydrophobicity on PTH receptor functional potency as measured by the cAMP (cyclic adenosine monophosphate) accumulation and β-arrestin recruitment assays. Among hydrophobic residues, we found that the Val2 position shows the least flexibility in terms of the SAR studies, whereas the Leu7 position appeared to be most flexible. Through circular dichroism and nuclear magnetic resonance spectroscopy studies, we were able to establish that changes in hydrophobic residues significantly change the extent of peptide helicity and that the helical character correlates well with receptor agonist activity. Here, we report several novel PTH 1-11 peptidomimetics that show comparable or enhanced potency to stimulate Gs-signaling over β-arrestin recruitment as compared with such properties of PTH 1-34 and the Parent Peptide.
Role for heparin-binding growth factors in glucose-induced vascular dysfunction. (1998)

Vascular hyperpermeability and excessive neovascularization are hallmarks of early and late vascular endothelial cell dysfunction induced by diabetes. Vascular endothelial growth factor (VEGF) appears to be an important mediator for these early and late vascular changes. We reported previously, using skin chambers mounted on backs of SD rats, that neutralizing antibodies directed against VEGF blocked vascular permeability and blood flow changes induced by elevated tissue glucose and sorbitol levels in a dosage-dependent manner. We report in this study, using the same skin chamber model and neutralizing antibodies directed against basic fibroblast growth factor (FGF-2), that another member of the heparin-binding growth factor family also mediates glucose- and sorbitol-induced vascular permeability and blood flow increases. In addition, we show that 1) TBC1635, a novel heparin-binding growth factor antagonist, blocks the vascular hyperpermeability and blood flow increases induced by elevated tissue levels of glucose and sorbitol and by topical application of VEGF and FGF-2 to granulation tissue in skin chambers, and 2) suramin, a commercially available growth factor antagonist, blocks glucose-induced vascular dysfunction. These results suggest an early role for heparin-binding growth factors in the vascular dysfunction caused by excessive glucose metabolism, possibly via the sorbitol pathway.
Ultra Long-Range Interactions between Large Area Graphene and Silicon (2014)

The wet-transfer of graphene grown by chemical vapor deposition (CVD) has been the standard procedure for transferring graphene to any substrate. However, the nature of the interactions between large area graphene and target substrates is unknown. Here, we report on measurements of the traction-separation relations, which represent the strength and range of adhesive interactions, and the adhesion energy between wet-transferred, CVD grown graphene and the native oxide surface of silicon substrates. These were determined by coupling interferometry measurements of the separation between the graphene and silicon with fracture mechanics concepts and analyses. The measured adhesion energy was 357 ± 16 mJ/m(2), which is commensurate with van der Waals interactions. However, the deduced traction-separation relation for graphene-silicon interactions exhibited a much longer range interaction than those normally associated with van der Waals forces, suggesting that other mechanisms are present.
Evidence for the location of the receptor-binding site of human erythropoietin at the carboxyl-terminal domain (1991)

Five different peptides (P1: 84-95; P2: 152-166; P3: 52-63; P4: 7-23; P5: 110-123) homologous to relatively hydrophilic regions of human erythropoietin (huEpo) have been synthesized to identify biologically active domains of the hormone. All peptides were able to induce high titers of peptide-specific antibodies in rabbits. Antisera from rabbits induced by recombinant huEpo (rhuEpo) contained a relatively high amount of antibodies preferentially directed against three peptides (P2, P4, and P5), of which P4 comprised the amino-terminal region, P2 the carboxyl-terminus, and P5 an interior region previously described as the receptor-binding site. The same three peptides were able to induce rhuEpo-specific antibodies, whereas P1 and P3 lacked this activity. Only peptide-P2-induced antisera inhibited the biologic activity of rhuEpo in a cell proliferation assay, indicating that the carboxyl-terminal region of the molecule is essentially involved in the biologic function of rhuEpo.
Abstract 2364: Spontaneous and vaccine-induced clearance of Mus Musculus Papillomavirus1 (MusPV1) infection (2016)

Abstract Human papilloma virus (HPV) high risk (hr) types cause several cancers, including cervical, vaginal, penile, and oropharyngeal, whereas low risk types cause benign diseases such as skin warts, anogenital warts and recurrent respiratory papillomatosis. Although hrHPV infection is one of the most common sexually transmitted diseases most infections remain asymptomatic and are cleared while a sub-population develops persistent HPV-related pathologies including cancer. Further, immune-compromised populations, notably organ transplant and HIV-positive patients, are particularly vulnerable to HPV-related pathologies. Here, we describe the first establishment of mouse papillomavirus-1 (MusPV1) disease in outbred and immune competent SKH1-Elite mice (Crl:SKH1-Hrhr). Challenge of SKH1 mice with MusPV1 resulted in three clinical outcomes: 1) persistent (&amp;gt;2 months) papillomas (∼15%), 2) transient papillomas that spontaneously regress typically within 2 months (∼10%), 3) no visible papillomas and viral clearance (∼75%). SKH1 mice with persisitent papillomas were treated using a potentially preventive and therapeutic DNA vaccine composed of human calreticulin (hCRT) linked to MusPV1 early proteins, mE6 and mE7 and the late protein mL2 (hCRTmE6/mE7/mL2). Three intramuscular DNA vaccinations (15 μg in PBS) via in vivo electroporation were administered weekly and immune responses were measured, including mE6/mE7/mL2 serum antibody response and T-cell epitope mapping studies. Previously persistent papillomas disappeared within 2 months after final vaccination. Clearance of MusPV1 was confirmed by loss of mE6/mE7 transcript staining using RNA-CISH on formalin-fixed, paraffin-embedded tail sections. Vaccination induced a strong mE6 and mE7 CD8+ T cell response in all mice. Interestingly, mL2 antibody responses were faster and stronger in asymptomatic challenged mice and in those that spontaneously cleared their papillomas after challenge as compared to mice with persistent papillomas. In sum, MusPV1 challenge of outbred, immune-competent SKH1 mice represents a promising model to further study potential immunotherapies for HPV-related disease and the relationship between spontaneous clearance of papillomavirus and host genetics. Citation Format: Rosie T. Jiang, Joshua W. Wang, Shiwen Peng, Chien-Fu Hung, Richard B.S Roden. Spontaneous and vaccine-induced clearance of Mus Musculus Papillomavirus1 (MusPV1) infection. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2364.
Determination of Capsaicin and Dihydrocapsaicin in Capsicum Fruit Samples using High Performance Liquid Chromatography (2011)

The aim of the present study was to determine the content of capsaicin and dihydrocapsaicin in Capsicum samples collected from city markets in Riyadh (Saudi Arabia), calculate their pungency in Scoville heat units (SHU) and evaluate the average daily intake of capsaicin for the population of Riyadh. The investigated samples consisted of hot chillies, red chillies, green chillies, green peppers, red peppers and yellow peppers. Extraction of capsaicinoids was done using ethanol as solvent, while high performance liquid chromatography (HPLC) was used for separation, identification and quantitation of the components. The limit of detection (LOD) of the method was 0.09 and 0.10 µg/g for capsaicin and dihydrocapsaicin, respectively, while the limit of quantification (LOQ) was 0.30 and 0.36 µg/g for capsaicin and dihydrocapsaicin, respectively. Hot chillies showed the highest concentration of capsaicin (4249.0 ± 190.3 µg/g) and the highest pungency level (67984.60 SHU), whereas green peppers had the lowest detected concentration (1.0 ± 0.9 µg/g); green peppers, red peppers and yellow peppers were non pungent. The mean consumption of peppers for Riyadh city population was determined to be 15.5 g/person/day while the daily capsaicin intake was 7.584 mg/person/day.
Evaluation of alternative presentation control techniques (2005)

Although slideshow presentation applications, such as PowerPoint™ have been popular for years, the techniques commercially available to control them rely on mouse and keyboard, which can be restrictive for the presenters. We evaluated two representative alternative designs of presentation control techniques - Bare Hand and Laser Pointer, through a Wizard-of-Oz user study. The result showed that Bare Hand was better than Laser Pointer and Standard (mouse/keyboard) control in terms of acceptance and preference from both presenters and audience. We also proposed design directions based on user feedback.
Surface-tension-driven multi-chip self-alignment techniques for heterogeneous 3D integration (2011)

Surface-tension-driven self-alignment (SA) is a promising technique for heterogeneous die-level stacking. Multiple dies can be manipulated in parallel at minimal cost. A defined amount of water present between the die and a carrier substrate is used to align the components. The minimization of the water-air interface is the driving force. Most studies were performed with a completely wetted chip surface with a resulting alignment of die periphery to carrier. This achieves a maximal die-pad to carrier-pad alignment quality equal to the dicing accuracy, which is typically ±25 μm. To further improve the pad-to-pad alignment accuracy, we propose a pad-assisted SA technique. With an initial placement quality of less than half a pad pitch, this technique achieves submicron SA accuracy. Furthermore, we extend the process to dies with Au studs needed in later thermo-compression bonding. Design rules to design a stable process are reported. A meniscus minimization model is built, which explains the experimental results and helps to design new SA patterns.
Part II: Recent Advances in Myocardial Contrast Echocardiography. Clinical Experience in the Detection of Coronary Artery Disease with Myocardial Contrast Echocardiography (2002)

Myocardial contrast enhancement following intravenous infusions or injections of perfluorocarbon‐containing microbubbles has now been observed consistently in humans. Currently, the major challenge facing us is interpreting accurately what we see. The myocardial contrast patterns we observe have, thus far, been shown to detect myocardial perfusion abnormalities during dipyridamole, adenosine, and dobutamine stress echocardiography. They also have been shown to detect zones of no reflow following coronary revascularization in patients with acute myocardial infarction. These preliminary data will require validation in larger multicenter clinical studies.
Longitudinal Monitoring Reveals Persistence of Colistin-Resistant Escherichia coli on a Pig Farm Following Cessation of Colistin Use (2022)

Colistin-resistant bacteria harboring plasmid-mediated mcr genes are of concern as they may be a cause of serious nosocomial infections. It is hypothesized that cessation of colistin use as a feed additive for pigs will reduce the occurrence and distribution of mcr genes in farms. The aim of this study was to investigate this hypothesis by longitudinal monitoring and characterizing of mcr positive Escherichia coli (MCRPE) isolates after colistin was withdrawn on a central Thailand pig farm that previously had a high frequency of MCRPE. Colistin use ceased at the beginning of 2017, and subsequently 170 samples were collected from farrowing sows and suckling piglets ( n = 70), wastewater ( n = 50) and farm workers ( n = 50) over a 3.5-year period. Bacteria were identified by MALDI-TOF mass spectrometry and minimal inhibitory concentrations were determined by broth microdilution. The antibiogram of mcr positive E. coli isolates was determined using the Vitek2 automated susceptibility machine, and multiplex and simplex PCRs were performed for mcr -1–8 genes. MCRPE containing either mcr -1 or mcr -3 were isolated from pigs throughout the investigation period, but with a declining trend, whereas MCRPE isolates were recovered from humans only in 2017. MCRPE were still being recovered from wastewater in 2020. Most MCRPE isolates possessed the virulence genes Stap, Stb , or Stx2e , reflecting pathogenic potential in pigs, and showed high rates of resistance to ampicillin, gentamicin and tetracycline. Pulsed-field gel electrophoresis and multi-locus sequence typing showed that diverse MCRPE clones were distributed on the farm. The study identified a decline of pathogenic MCRPE following withdrawal of colistin, with pigs being the primary source, followed by wastewater. However, short-term therapeutic usage of other antibiotics could enhance the re-occurrence of mcr- carrying bacteria. Factors including the environment, management, and gene adaptations that allow maintenance of colistin resistance require further investigation, and longer-term studies are needed.
Neuroimmune mechanisms in health and disease: 1. Health. (1996)

A novel scientific discipline that examines the complex interdependence of the neural, endocrine and immune systems in health and disease has emerged in recent years. In health, the neuroimmunoregulatory network is fundamental to host defence and to the transfer of immunity to offspring; the network also plays important roles in intestinal physiology and in tissue regeneration, healing and reproduction. The proliferation of lymphocytes in primary lymphoid organs (bone marrow, bursa of Fabricius [in birds] and thymus) and in secondary lymphoid organs (spleen, lymph nodes and mucosal lymphoid tissue) depends on prolactin and growth hormone. These hormones allow immune cells to respond to antigen and to soluble mediators, called cytokines. Immune-derived cytokines are capable of inducing fever and of altering neuro-transmitter activity in the brain and hormone secretion by the pituitary gland. The activation of the hypothalamus-pituitary-adrenal axis by cytokines leads to immunosuppression. Lymphoid organs are innervated, and tissue mast cells respond to neurologic stimuli. In general, acetylcholine and substance P exert immunostimulatory and proinflammatory effects, whereas epinephrine and somatostatin are immunosuppressive and anti-inflammatory. In this article, the authors predict that novel approaches to immunomodulation will be possible by altering the level or efficacy of immunoregulatory hormones and neurotransmitters.
Direct Observation of Acyl Azide Excited States and Their Decay Processes by Ultrafast Time Resolved Infrared Spectroscopy (2009)

The photochemistry of three carbonyl azides was studied by ultrafast time-resolved IR spectroscopy. Benzoyl, 2-naphthoyl, and pivavoyl azides are promoted to upper excited states S(n) with 270 nm excitation in chloroform. The S(n) states decay in 300 fs to form both the carbonylnitrenes and the S(1) excited states. The decay of the S(1) states of the carbonyl azides correlates with the growth of isocyanates. Formation of carbonylnitrene from S(1) is at most a minor process if it happens at all. The quantum yields of azide decomposition of these azides with 270 nm light are close to unity in chloroform.
Evaluation and Management of Primary Vaginal Penetration Failure (2003)

Objective: To determine and analyze the etiologies and modalities of treatment for unconsummated coitus due to vaginal penetration failure.
Material(s) and Method(s): This retrospective study investigated 212 couples, i.e., sexual partners, who visited our offices because of unconsummated coitus due to failure to penetrate the vagina, of them, 129 couples completed the full course of treatment and follow-up. A team consisting of a gynecologist, urologist, psychiatrist, and sex counselor was responsible for the diagnoses and treatments. We analyzed the individual causes and compared the results.
Results: Primary vaginal penetration failures were divided into six categories of causes: vaginismus (49%), poor sexual knowledge or technique (31%), premature ejaculation, erectile dysfunction, sexual aversion/phobia, and congenital abnormalities. The success rates of treatment were 93.3%, 100%, 83.3%, 83.3%, 75%, and 100%, respectively.
Conclusion(s): Among the couples with unconsummated coitus, the two leading causes of vaginal penetration failure were found to be vaginismus and lack of sex information. Furthermore, most cases of vaginismus were due to psychological factors, which also contributed to vaginal penetration failure due to other causes. Thus, it was possible to resolve these underlined causes under the treatment strategies recommended by the team.
Dual-Band Infrared Video-Based Measurement Using Pulse Wave Maps to Analyze Heart Rate Variability (2018)

Remote photoplethysmography (rPPG) enables us to capture the vital signs such as pulse rate, respiratory rate, oxygen saturation, and even heart rate variability (HRV) without any contact devises. Although the papers of rPPG mainly focus on the use of standard RGB camera, it cannot used for the cases in night or under the dim light conditions. Therefore, in this paper, we propose a novel noncontact method for monitoring HRV without visible lighting. The proposed method uses dual-band infrared videos to ensure robustness to fluctuations in illumination. The hemoglobin component is extracted via a simple projection from the dual-band pixel values in logarithmic space. We demonstrate the accurate extraction of pulse wave signals using pulse wave maps. As the results, we indicated the effectiveness of HRV monitoring in the situation under the dim light condition. &#xA9; 2018 Society for Imaging Science and Technology.
The Role of Metal Induced Oxidation for Copper Deposition on Silicon Surface (1997)

Cu deposition behavior onto Si surfaces was investigated as a function of dipping time in various chemical solutions. It shows the progressive phenomena for Cu deposition onto Si surfaces from the initial reaction to final equilibrium state so that we can interpret the different Cu deposition behavior in solutions by evaluating chemical nature, Cu dissolution effect, Cu particle growing effect, chemical oxidation, and metal induced oxidation (MIO) which take place in Cu deposition process. In this work, we categorize the Cu deposition process into three stages such as initial stage, progressive stage, and equilibrium stage. The different initial behavior of Cu deposition is explained by the different ionic strength of chemicals that is mainly attributed to mass transport. Cu particle growth is a main cause of Cu deposition with high concentration and determined on the base of the relation between Cu particle growth rate and dissolution rate depending on pH and redox potential values of chemicals. Oxide formation due to chemical oxidation and metal induced oxidation hinders Cu deposition and metal Cu particle growth and it causes the Cu deposition to be saturated with a self‐limiting effect. We found that the critical hindrance oxide thickness for Cu deposition and Cu particle growth is about 3 Å at which one monolayer transition layer of silicon dioxide is estimated. Consequently, we modeled Cu deposition behavior in various solutions as a function of dipping time.