gebhart/patrepeval huggingface dataset:
The specificity of clostripain from Clostridium histolyticum (1994)

The S' subsite specificity of clostripain from Clostridium histolyticum was investigated by acyl transfer to libraries of amino acid amides, Ala-Xaa dipeptides, proline derivatives and pentapeptides using N alpha-benzoyl-L-arginine ethyl ester as acyl donor. A pentapeptide library consisting of 29 pentapeptides with general structure Xaa-Ala-Ala-Ala-Gly, Ala-Xaa-Ala-Ala-Gly and Ala-Ala-Xaa-Ala-Gly, where Xaa represents Gly, Ala, Pro, Leu, Phe, Asp, Glu, Arg and Lys, was prepared by solid-phase synthesis. The data analysis was performed by HPLC and evaluated by statistical algorithms. The nucleophile efficiency covers a range of more than three orders of magnitude. In the P'1 position, low specificity for amino acid amides and Xaa-(Ala)3-Gly peptides was found, however, in the P'2 position, positively charged amino acid residues are strongly preferred. The negatively charged side chains of aspartic acid and glutamic acid in the P'1 and P'2 positions, respectively, show only poor nucleophilic behaviour. In the case of these amino acids, the S'-P' interactions depend significantly on their position of these residues in the peptide chain of the nucleophile. The transfer of aspartic acid and glutamic acid from P'1-P'3 increases the nucleophile efficiency by approximately two orders of magnitude. The aromatic side chains are not well accepted, especially in the case of P'3Phe. Surprisingly, P'1Gly leads to effective P'-S' interactions. However, the opposite result was obtained for P'2Gly. The high efficiency for Gly-NH2 does not fit with the hydrophobicity structure/activity relationships. In most cases, peptide chain elongation does not improve the nucleophile efficiency. The effective interaction of D-Leu-NH2 with the S' subsite of clostripain emphasizes the fact that the nucleophile stereospecificity is not restricted to L-amino acids. The results with proline derivatives indicate remarkably different specificities of the S' binding site which can only be explained by conformational restraints. A positive cooperativity between P'1Pro and P'2Gly and a negative cooperativity between P'1Pro and P'2Phe was observed. The arrangement of three proline residues next to each other represents a favourable conformation for effective enzyme-nucleophile interactions.
Fission of collapsing cavitation bubbles (2002)

High-speed observations clearly show that though a collapsing cavitation bubble approaches its minimum size as a coherent single volume, it usually reappears in the first rebounding frame as a cloud of much smaller bubbles or as a highly distorted single volume. This paper explores two mechanisms that may be responsible for that bubble fission process, one invoking a Rayleigh–Taylor stability analysis and the other using the so-called microjet mechanism. Both approaches are shown to lead to qualitatively similar values for the number of fission fragments and the paper investigates the flow parameters that effect that number. Finally, the additional damping of the Rayleigh–Plesset single-bubble calculation caused by the fission process is investigated; it is shown that the fission damping dominates other contributions normally considered and is consistent with the number of collapses and rebounds that are observed to occur in experiments.
Measurement of the Soft-Drop Jet Mass in pp Collisions at s=13  TeV with the ATLAS Detector (2018)

Jet substructure observables have significantly extended the search program for physics beyond the standard model at the Large Hadron Collider. The state-of-the-art tools have been motivated by theoretical calculations, but there has never been a direct comparison between data and calculations of jet substructure observables that are accurate beyond leading-logarithm approximation. Such observables are significant not only for probing the collinear regime of QCD that is largely unexplored at a hadron collider, but also for improving the understanding of jet substructure properties that are used in many studies at the Large Hadron Collider. This Letter documents a measurement of the first jet substructure quantity at a hadron collider to be calculated at next-to-next-to-leading-logarithm accuracy. The normalized, differential cross section is measured as a function of log_{10}ρ^{2}, where ρ is the ratio of the soft-drop mass to the ungroomed jet transverse momentum. This quantity is measured in dijet events from 32.9 fb^{-1} of sqrt[s]=13 TeV proton-proton collisions recorded by the ATLAS detector. The data are unfolded to correct for detector effects and compared to precise QCD calculations and leading-logarithm particle-level Monte Carlo simulations.
Abstract: Correction of the Lower Lip with a Cartilage Graft and Lip Resection in Patients with Facioscapulohumeral Muscular Dystrophy (2016)

INTRODUCTION: Facioscapulohumeral muscular dystrophy (FSHD) is a myopathy that involves facial, shoulder, and upper arm muscles. FSHD is a rare disease and there are few reports in the literature describing the correction of the associated facial deformities. Recently, we surgically treated three patients with FSHD who complained of functional and aesthetic issues due to a drooping lower lip caused by facial muscle atrophy and weakness. MATERIALS AND METHODS: All procedures were performed under local anesthesia. After resection of the atrophic and drooping central part of the lower lip, approximately 1–2 cm in width, we created an oblong subcutaneous space for grafting the auricular cartilage through the lip resection area and a small horizontal incision under the mental region. To avoid the outline of the grafted cartilage appearing on the skin surface, and to fix the lower part of the cartilage to the mandibular bone, the space was made through the atrophic orbicularis oris muscle, just above the periosteum of the mandible. RESULTS: There are some reports describing the correction of the lower lip using an atrophic lip resection,1 free muscle transfer, 2, 3 muscle transition,4 lifting by fascia or absorbable suture,5 or hard tissue grafting. We treated three patients with a novel technique utilizing an auricular cartilage graft to lift the atrophic and drooping lower lip. After the operation, the lower lip was elevated in all patients. CONCLUSION: An auricular cartilage graft with lip resection was performed for patients with FSHD who suffered from a drooping lower lip. This method enables the elevation of the lower lip via a short operation that utilizes local anesthesia. After the operation, the patient may achieve better functional and aesthetic outcomes. This procedure may be considered in future cases requiring correction of a drooping lip. DISCLOSURE/FINANCIAL SUPPORT:None of the authors has a financial interest in any of the products, devices, or drugs mentioned in this manuscript. REFERENCES: 1. Kamiishi H, Ohtsuka H, Shioya N. Correction of myopathic face associated with myotonic muscular dystrophy. A case report. J Maxillofac Surg 1977;5:48–54 2. Ueda K, Oba S, Ohtani K, et al. Functional lower lip reconstruction with a forearm flap combined with a free gracilis muscle transfer. J Plast Reconstr Aesthet Surg 2006;59:867–870 3. Ninkovic M, Spanio di Spilimbergo S, Ninkovic M. Lower lip reconstruction: Introduction of a new procedure using a functioning gracilis muscle free flap. Plast Reconstr Surg 2007;119:1472–1480 4. Chan RK, Bojovic B, Talbot SG, et al. Lower lip suspension using bilateral temporalis muscle flaps and fascia lata grafts. Plast Reconstr Surg 2012;129:119–122 5. Cocke WM, Davis WG. Reconstruction in Landouzy-Dejerine progressive muscular dystrophy. Plast Reconstr Surg 1971;48:77–79
Optical Methods in Sensing and Imaging for Medical and Biological Applications (2019)

The recent advances in optical sources and detectors have opened up new opportunities for sensing and imaging techniques which can be successfully used in biomedical and healthcare applications. This book, entitled &lsquo;Optical Methods in Sensing and Imaging for Medical and Biological Applications&rsquo;, focuses on various aspects of the research and development related to these areas. The book will be a valuable source of information presenting the recent advances in optical methods and novel techniques, as well as their applications in the fields of biomedicine and healthcare, to anyone interested in this subject.
Picosecond 1.3-μm bismuth fibre laser mode-locked by a nonlinear loop mirror (2016)

The influence of the concentration of bismuth active centres (BACs) in phosphosilicate fibres on their optical parameters, including gain coefficient and non-saturable losses, has been studied. A range of BAC concentrations optimal for designing ultrashort-pulse (USP) lasers was chosen based on the obtained results. The optimised fibre was used to fabricate an all-fibre USP laser mode-locked by a nonlinear loop mirror, which emits pulses with an energy of and a repetition rate of . A bismuth fibre amplifier made it possible to increase the pulse energy to . After compression in a diffraction grating compressor, the pulse duration decreased to .
Direct Assembly and Metal-Ion Binding Properties of Oxytocin Monolayer on Gold Surfaces (2019)

Peptides are very common recognition entities that are usually attached to surfaces using multistep processes. These processes require modification of the native peptides and of the substrates. Using functional groups in native peptides for their assembly on surfaces without affecting their biological activity can facilitate the preparation of biosensors. Herein, we present a simple single-step formation of native oxytocin monolayer on gold surface. These surfaces were characterized by atomic force spectroscopy, spectroscopic ellipsometry, and X-ray photoelectron spectroscopy. We took advantage of the native disulfide bridge of the oxytocin for anchoring the peptide to the Au surface, while preserving the metal-ion binding properties. Self-assembled oxytocin monolayer was used by electrochemical impedance spectroscopy for metal-ion sensing leading to subnanomolar sensitivities for zinc or copper ions.
Monitoring microbial product synthesis by measurement of the dehydrogenase activity (1988)

Abstract A method for the photometric measurement of dehydrogenase activities with the redox dye phenazine methosulphate at a fixed biomass concentration was applied for the investigation of idiophasic product synthesis. It was found that in citric acid fermentation by Yarrowia lipolytica which is characterized by a well defined separation into tropho‐and idiophase the magnitude of product synthesis rates corresponds to the level of dehydrogenase activity at the end of the trophophase. In cellulase production by Trichoderma reesei the tropho‐and idiophase are not well defined but a rise of dehydrogenase activity in the course of the idiophase is likely to correspond to an increase of the cellulase formating rate. The significance of the relation of dehydrogenase activity to production rates for monitoring industrial fermentations is discussed.
Case 20-1967 (1967)

Presentation of CaseA nineteen-year-old girl entered the hospital because of fever and a heart murmur.She had been well until nineteen days previously, when she began to experience myalgia, malaise, fever and a headache. Four days before that time she had scratched some pustules over the right eyebrow and cheek. The symptoms persisted, and the temperature rose to 104°F. on the day after their onset. On admission to another hospital on the following day a stiff neck was found, and she was intermittently delirious. The hematocrit was 37 per cent, and the white-cell count 8400, with 61 per cent . . .
Mesothelial cell inclusions within mediastinal lymph nodes (1994)

The presence of mesothelial cell inclusions within mediastinal lymph nodes is an extremely rare occurrence with apparently only two previously reported cases. We report a single case with immunohistochemistry and transmission electron microscopy. A study of 318 mediastinal nodes from 80 patients using haematoxylin and eosin and immunohistochemistry is reported with the observation of no further positive cases. A review of the literature concerning nodal inclusions found at other anatomical sites aids discussion on the aetiology of this type of nodal inclusion.
Characteristics of early‐onset pancreatic cancer and its association with familial pancreatic cancer and hereditary pancreatic cancer syndromes (2020)

The incidence of pancreatic cancer is high among those in their sixties to seventies but low in those in their fifties or younger. Although there is no unified definition regarding the age of early-onset pancreatic cancer, previously published reports suggest that, compared to later-onset pancreatic cancer patients, early-onset pancreatic cancer patients tend to be detected at advanced stages and thus have poor prognoses, but they do not show significantly higher rates of patients with genetic factors. On the other hand, it has been reported that patients with familial pancreatic cancer and hereditary pancreatic cancer syndromes often develop pancreatic cancer at a young age. The broad definition of familial pancreatic cancer is pancreatic cancer in patients who have two or more first-degree relatives with pancreatic cancer; whereas the narrow definition of familial pancreatic cancer is the broad definition of familial pancreatic cancer, while excluding those with inherited tumor syndromes. Hereditary tumors developing pancreatic cancer include hereditary pancreatitis, hereditary breast and ovarian cancer, Peutz-Jeghers syndrome, familial atypical multiple mole melanoma syndrome, familial adenomatous polyposis, and hereditary non-polyposis colorectal cancer, all of which are autosomal dominant hereditary diseases. This study reviews the clinical characteristics of early-onset pancreatic cancer and its association with familial pancreatic cancer and hereditary pancreatic cancer syndromes.
Diffusion Tensor Imaging of Frontal White Matter and Executive Functioning in Cocaine-Exposed Children (2006)

Prenatal cocaine exposure, alone and in combination with exposure to other drugs, is associated with slightly poorer executive functioning and subtle microstructural changes suggesting less mature development of frontal white matter pathways. The relative contribution of postnatal environmental factors, including characteristics of the caregiving environment and stressors associated with poverty and out-of-home placement, on brain development and behavioral functioning in polydrug-exposed children awaits further research.
From Manual Android Tests to Automated and Platform Independent Test Scripts (2016)

Because Mobile apps are extremely popular and often mission critical nowadays, companies invest a great deal of resources in testing the apps they provide to their customers. Testing is particularly important for Android apps, which must run on a multitude of devices and operating system versions. Unfortunately, as we confirmed in many interviews with quality assurance professionals, app testing is today a very human intensive, and therefore tedious and error prone, activity. To address this problem, and better support testing of Android apps, we propose a new technique that allows testers to easily create platform independent test scripts for an app and automatically run the generated test scripts on multiple devices and operating system versions. The technique does so without modifying the app under test or the runtime system, by (1) intercepting the interactions of the tester with the app and (2) providing the tester with an intuitive way to specify expected results that it then encode as test oracles. We implemented our technique in a tool named Barista and used the tool to evaluate the practical usefulness and applicability of our approach. Our results show that Barista can faithfully encode user defined test cases as test scripts with built-in oracles, generates test scripts that can run on multiple platforms, and can outperform a state-of-the-art tool with similar functionality. Barista and our experimental infrastructure are publicly available.
Functional histology of quill erection in the porcupine, Erethizon dorsatum (1997)

The histology of the porcupine's skin and subcutis is described. The functional relationships of the thoracic skin during elevation of the quills involve a smooth arrector muscle attached to quill sets, one set behind the other, with the muscle at a slant usually from a single root tip of one set to the distal part of the follicles in the caudal set. Stretched elastin returns the quills to their resting position. There is a low-resistance pathway for the tilting quill roots through loose connective tissue and fat until a collagenous strand attached to the quill set stops further tilt. The lumbosacral region (rosette) has a two-layered arrector, but it attaches to only its own quill set and inserts into the dermis. Both regions have a varied and complicated system of transverse and oblique muscles associated with the roots in a set. (The occurrence of obliques is variable in the thoracic region.) A hypothesis is presented concerning the mechanism of quill detachment from the porcupine after the quill is rammed into a predator. This involves the shearing of the conical root tip along its adherent follicular cells and a stopping device (spool) to prevent the root from self-stabbing.
Partial Oral versus Intravenous Antibiotic Treatment of Endocarditis (2018)

BACKGROUND Patients with infective endocarditis on the left side of the heart are typically treated with intravenous antibiotic agents for up to 6 weeks. Whether a shift from intravenous to oral antibiotics once the patient is in stable condition would result in efficacy and safety similar to those with continued intravenous treatment is unknown. METHODS In a randomized, noninferiority, multicenter trial, we assigned 400 adults in stable condition who had endocarditis on the left side of the heart caused by streptococcus, Enterococcus faecalis, Staphylococcus aureus, or coagulase-negative staphylococci and who were being treated with intravenous antibiotics to continue intravenous treatment (199 patients) or to switch to oral antibiotic treatment (201 patients). In all patients, antibiotic treatment was administered intravenously for at least 10 days. If feasible, patients in the orally treated group were discharged to outpatient treatment. The primary outcome was a composite of all-cause mortality, unplanned cardiac surgery, embolic events, or relapse of bacteremia with the primary pathogen, from the time of randomization until 6 months after antibiotic treatment was completed. RESULTS After randomization, antibiotic treatment was completed after a median of 19 days (interquartile range, 14 to 25) in the intravenously treated group and 17 days (interquartile range, 14 to 25) in the orally treated group (P=0.48). The primary composite outcome occurred in 24 patients (12.1%) in the intravenously treated group and in 18 (9.0%) in the orally treated group (between-group difference, 3.1 percentage points; 95% confidence interval, −3.4 to 9.6; P=0.40), which met noninferiority criteria. CONCLUSIONS In patients with endocarditis on the left side of the heart who were in stable condition, changing to oral antibiotic treatment was noninferior to continued intravenous antibiotic treatment.
Design and fabrication of broadband thin-film lithium niobate phase modulators (2024)

Despite the present ubiquity of lithium niobate (LiNbO3) in fiber-optic telecommunications and its attractive nonlinear electro-optic (EO) properties, the evolution of LiNbO3 integrated photonics lags behind that of its silicon (Si) and III-V material platforms. Discrete devices fabricated in bulk single-crystal LiNbO3 generally rely on low-index-contrast optical waveguides with large bend radii [1] and specialized micromachining processes to sustain broadband operation [2], which inhibits dense integration. A number of existing thin-film LiNbO3 devices, however, demonstrate that there is potential for further development and suggest a way to surmount some of the disadvantages inherent to bulk LiNbO3. With the recent widespread availability of full 75 mm wafers of crystal-ion-sliced (CIS) thin-film LiNbO3 from a number of distributors, there has been a plethora of LiNbO3 device research and innovation since the early 2010s [3], [4]. ☐ Notable devices that leverage the high-index-contrast provided by a thin LiNbO3 device layer include tunable ring resonators [5], Mach-Zehnder interferometers [6], switches [7], and standalone phase modulators [6], [8]–[10]. Developed in parallel to these devices are various hybrid devices that rely on either Si [11]–[16] or silicon nitride (Si3N4) [15], [17], [18] for loading and guiding an optical mode. A common feature of all devices mentioned herein is reduced optical mode size. This reduced mode size leads to devices with vastly improved electro-optic activity over their bulk predecessors, resulting most notably in reduced modulator half-wave voltages. Coupling the reduced half-wave voltage length products with the ability to bend and fold the high-index-contrast optical waveguides results in a substantially decreased device footprint ideal for future integrated photonic systems. ☐ The focus of this work is on broadband phase modulators in thin-film LiNbO3 which until now have not been investigated outside of bulk LiNbO3. The first challenge is to obtain thin films of LiNbO3 with a consistent sub-10 µm thickness. Mechanical thinning is investigated and implemented; however, thickness variation on the order of 2 to 3 µm results in inconsistent velocity matching and therefore reduced bandwidths in fabricated devices. This variation necessitates the development of a tuning method that allows broadband mechanically-thinned devices to be repeatably produced. After investigation of mechanically-thinned substrates, this work focuses on CIS-based phase modulators. In CIS substrates, a high-conversion-efficiency device is developed which exhibits a measured EO response up to an unprecedented 500 GHz.
Randomized trial to evaluate contraceptive efficacy, safety and acceptability of a two-rod contraceptive implant over 4 years in the Dominican Republic (2019)

WHO prequalification allows global donors to procure Sino-implant (II), which means women in many low resource countries will have greater access to highly effective and acceptable contraceptive implants. Our study noted important clinical differences, including shorter duration of high effectiveness with Sino-implant (II) when compared to the other available two-rod system, Jadelle®. Introduction strategies should include appropriate training on these differences.
Compressive stress relaxation behavior of irradiated ultra‐high molecular weight polyethylene at 37°C (1994)

The preconditioned stress relaxation behavior of irradiated ultra-high molecular weight polyethylene (UHMWPE), a commonly used bearing surface in total joint replacements (TJR), was modelled in uniaxial compression at 37 degrees C. Twenty cylindrical specimens (10 mm dia. x 27 mm length) were machined from a compression molded plate of medical grade UHMWPE and gamma-irradiated to a minimum dose of 2.5 Mrad. At an initial strain rate 1000%/s, five specimens were each tested at constant strains of 1, 2, 5, and 10%. The modified superposition principle provided a good agreement of the nonlinear viscoelastic (stress relaxation) behavior of UHMWPE (standard error of 0.0753 MPa).