gebhart/patrepeval huggingface dataset:
Active site mutant Glu-43 .fwdarw. Asp in staphylococcal nuclease displays nonlocal structural changes (1990)

The crystal structure of the Glu-43----Asp mutant of staphylococcal nuclease complexed with Ca2+ and the inhibitor thymidine 3',5'-bisphosphate (pdTp) has been determined and refined by restrained least-squares methods to a conventional crystallographic R value of 0.174 at a resolution of 1.74 A. Throughout most of the structure, the conformation of the backbone atoms of the mutant is similar to that of the wild-type protein; however, the seemingly conservative mutation Glu----Asp has significantly perturbed the structure of a loop adjacent to the active site, as well as giving rise to looser binding of the essential calcium ion and to a less extensive network of bound water molecules in the active site. Crystal contacts that extend into the active site have also been altered by this amino acid substitution. The changes caused by this mutation are considerably more drastic than would have been predicted and should serve as caveats to those who would draw conclusions about structure-function relationships on the basis of site-directed mutagenesis experiments in the absence of structural data.
Follow-up of Stented Carotid Arteries by Doppler Ultrasound (2002)

OBJECTIVE Blood flow velocity (BFV) in the carotid artery is altered by stent placement. The significance of these alterations is unknown. In our experience, both standard BFV criteria for stenosis and customized criteria recommended by other authors have led to high rates of false-positive studies. We reviewed our experience with Doppler ultrasonography immediately after extracranial carotid artery stent placement to define criteria for restenosis by BFV. METHODS Complete carotid angiograms and BFV results were available for 114 patients treated between January 1998 and December 1999. Angiographic images obtained immediately after stent placement and at follow-up were measured for residual or recurrent stenosis by a blinded reviewer according to the North American Symptomatic Carotid Endarterectomy Trial method. Results of BFV studies obtained within 1 week of stent placement were interpreted by using two standard criteria (A, peak in-stent systolic velocity greater than 125 cm/s;B, internal carotid artery-to-common carotid artery ratio greater than 3.0) and two customized criteria (C, peak in-stent velocity greater than 170 cm/s;D, internal carotid artery-to-common carotid artery ratio greater than 2.0). The results of follow-up angiography and the most recent Doppler study were compared for nine patients. RESULTS On the basis of an examination of Doppler studies obtained immediately after stent placement, 36 patients met Criterion A for stenosis according to measured BFV (corresponding mean angiographic stenosis, 14.73 ± 18.45%), 3 patients met Criterion B (mean stenosis, 1.67 ± 2.89%), 8 patients met Criterion C (mean stenosis, 12.61 ± 13.18%), and 14 met Criterion D (mean stenosis, 7.98 ± 21.74%). No patient with Doppler criteria for significant stenosis had more than 50% residual stenosis. Three of nine patients who underwent follow-up angiography had stenosis of 50% or more; of these three patients, two underwent second angioplasty procedures. The peak in-stent systolic velocity or internal carotid artery-to-common carotid artery BFV ratio for each of the three patients with restenosis, but not for the six other patients, had increased by more than 80% since the immediate post-stenting Doppler study. CONCLUSION Strict BFV criteria for restenosis after carotid artery stenting are less reliable than change in BFV over time. An immediate post-stenting Doppler study must be obtained to serve as a reference value for future follow-up evaluation.
Symbolic Program Analysis in Almost-Linear Time (1982)

This paper describes an algorithm to construct, for each expression in a given program text, a symbolic expression whose value is equal to the value of the text expression for all executions of the program. We call such a mapping from text expressions to symbolic expressions a cover. Covers are useful in such program optimization techniques as constant propagation and code motion. The particular cover constructed by our methods is in general weaker than the covers obtainable by the methods of [Ki], [FKU], [RL], [R2] but our method has the advantage of being very efficient. It requires $O(m\alpha (m,n) + l)$ operations if extended bit vector operations have unit cost, where n is the number of vertices in the control flow graph of the program, m is the number of edges, l is the length of the program text, and $\alpha $ is related to a functional inverse of Ackermann’s function [T2]. Our method does not require that the program be well-structured nor that the flow graph be reducible.
Elimination of plasmids by new 4-quinolones (1985)

Nalidixic acid and six of the new 4-quinolones eliminated F'lac and various native R plasmids from Escherichia coli at one half or one quarter the MIC. Four of eight plasmids tested were cured by all derivatives, with frequencies from 10 to 98%. Quinolones did not eliminate all plasmids that were cured by novobiocin, and vice versa.
Low-Delay Signal Processing for Digital Hearing Aids (2010)

Digital signal processing in modern hearing aids is typically performed in a subband or transform domain that introduces analysis-synthesis delays in the forward path. Long forward-path delays are not desirable because the processed sound combines with the unprocessed sound that arrives at the cochlea through the vent and changes the sound quality. Nonetheless, subband domain processing for digital hearing aids is the most popular choice for hearing aids because of the associated computational simplicity. In this paper, we present an alternative digital hearing aid structure with low-delay characteristics. The central idea in the paper is a low-delay spectral gain shaping method (SGSM) that employs parallel parametric equalization (EQ) filters. The low-delay SGSM provides frequency-dependent amplification for hearing loss compensation with low forward path delays and performs dynamic signal processing such as noise suppression and dynamic range compression. Parameters of the parametric EQ filters and associated gain values are selected using a least-squares approach to obtain the desired spectral response. The low-delay structure also employs an off-the-forward-path, frequency domain adaptive filter to perform acoustic feedback cancellation. Extensive MATLAB simulations and subjective evaluations of the results indicate that the method of this paper is competent with a state-of-the-art digital hearing aid system, but exhibits much smaller forward-path delays.
“Pincer” Pyridine–Dicarbene–Iridium Complexes: Facile CH Activation and Unexpected η<sup>2</sup>‐Imidazol‐2‐ylidene Coordination (2008)

A bridge to somewhere: A series of pyridine dicarbene iridium “pincer” complexes is easily accessible when pyridine ring metalation is suppressed by methyl substitution (see structure; NHC=N-heterocyclic carbene). A new bridging binding mode of the imidazol-2-ylidene heterocycle, involving η2-alkene-like coordination, has been observed crystallographically.
Shallow <i>p</i>+ junction formation by a reverse-type dopant preamorphization scheme (1989)

Device grade ultrashallow p+ junctions have been fabricated by a novel ion implantation scheme. The novelty of the method is in using antimony to amorphize silicon prior to a low-energy boron implantation. Antimony satisfies a combination of two requirements lacking from all previously applied preamorphization schemes. First, due to the heavy mass of antimony, amorphization of silicon is achieved with a minimal amount of implantation damage. Second, and most important, antimony is a dopant of an opposite type than boron. Because of this, the inevitable implant tail of the preamorphizing species serves to confine the depth of the p layer. The optimized conditions for the application of this scheme have been determined. Junctions below 100 nm in depth, with less than 200 Ω/⧠ sheet resistance and junction leakage of 10 nA/cm2, have been achieved. The electrical results have been correlated with the residual defect structure observed by cross-sectional transmission electron microscopy.
Deep Gaussian Embedding of Graphs: Unsupervised Inductive Learning via Ranking (2018)

Methods that learn representations of nodes in a graph play a critical role in network analysis since they enable many downstream learning tasks. We propose Graph2Gauss - an approach that can efficiently learn versatile node embeddings on large scale (attributed) graphs that show strong performance on tasks such as link prediction and node classification. Unlike most approaches that represent nodes as point vectors in a low-dimensional continuous space, we embed each node as a Gaussian distribution, allowing us to capture uncertainty about the representation. Furthermore, we propose an unsupervised method that handles inductive learning scenarios and is applicable to different types of graphs: plain/attributed, directed/undirected. By leveraging both the network structure and the associated node attributes, we are able to generalize to unseen nodes without additional training. To learn the embeddings we adopt a personalized ranking formulation w.r.t. the node distances that exploits the natural ordering of the nodes imposed by the network structure. Experiments on real world networks demonstrate the high performance of our approach, outperforming state-of-the-art network embedding methods on several different tasks. Additionally, we demonstrate the benefits of modeling uncertainty - by analyzing it we can estimate neighborhood diversity and detect the intrinsic latent dimensionality of a graph.
Gastrin and somatostatin in Helicobacter pylori infected antral mucosa. (1994)

Helicobacter pylori infection is associated with increased meal stimulated gastrin secretion, but the reason for this is unknown. Sequence specific radioimmunoassays were used to measure the concentration of alpha-amidated gastrin, the total progastrin product, and somatostatin in biopsy specimens of human antral mucosa. The antral concentrations of alpha-amidated gastrin and of total progastrin products were significantly higher in H pylori infected patients than in those not infected by this organism. In contrast, the antral somatostatin concentration was significantly decreased in infected patients. Progastrin processing, determined by gel chromatography, seemed unaffected by H pylori infection. The results suggest that the finding of increased gastrin secretion from the antral G cells in H pylori infected patients may be a result of reduced inhibition of G-cell secretion by somatostatin.
Determining the Accuracy of Crowdsourced Tweet Verification for Auroral Research (2016)

<p class="p1">The Aurorasaurus project harnesses volunteer crowdsourcing to identify sightings of an aurora (the “northern/southern lights”) posted by citizen scientists on Twitter. Previous studies have demonstrated that aurora sightings can be mined from Twitter with the caveat that there is a large background level of non-sighting tweets, especially during periods of low auroral activity. Aurorasaurus attempts to mitigate this, and thus increase the quality of its Twitter sighting data, by using volunteers to sift through a pre-filtered list of geolocated tweets to verify real-time aurora sightings. In this study, the current implementation of this crowdsourced verification system, including the process of geolocating tweets, is described and its accuracy (which, overall, is found to be 68.4%) is determined. The findings suggest that citizen science volunteers are able to accurately filter out unrelated, spam-like, Twitter data but struggle when filtering out somewhat related, yet undesired, data. The citizen scientists particularly struggle with determining the real-time nature of the sightings, so care must be taken when relying on crowdsourced identification.
Unsynchronized 4D barcodes: coding and decoding time-multiplexed 2D colorcodes (2007)

Abstract. We present a novel technique for optical data transfer between public displays and mobile devices based on unsynchronized 4D barcodes. We assume that no direct (electromagnetic or other) connection between the devices can exist. Time-multiplexed, 2D color barcodes are displayed on screens and recorded with camera equipped mobile phones. This allows to transmit information optically between both devices. Our approach maximizes the data throughput and the robustness of the barcode recognition, while no immediate synchronization exists. Although the transfer rate is much smaller than it can be achieved with electromagnetic techniques (e.g., Bluetooth or WiFi), we envision to apply such a technique wherever no direct connection is available. 4D barcodes can, for instance, be integrated into public web-pages, movie sequences, advertisement presentations or information displays, and they encode and transmit more information than possible with single 2D or 3D barcodes. 1
Conformational Fluctuations in Deoxy Hemoglobin Revealed as a Major Contributor to Anionic Modulation of Function through Studies of the Oxygenation and Oxidation of Hemoglobins A<sub>0</sub> and Deer Lodge β2(NA2)His → Arg (1998)

Organisms rely on regulation at the molecular level, such as the allosteric regulation of hemoglobin (Hb) function by anions, to meet challenges presented by changing environmental and physiological conditions. A comparison of the effects of anions on oxygenation, oxidation, and sulfhydryl reactivity of Hb leads us to suggest that a large and significant part of the shift in oxygen affinity brought about by anion binding occurs as a result of increased conformational rigidity of the T state of deoxy Hb. As conformational rigidity increases, it becomes increasingly difficult for subunits in the deoxygenated T-state tetramer to assume higher oxygen affinity forms (T', T", T"'...) with less steric hindrance. The oxygen affinity reflects the average of the rapidly equilibrating conformations within the T state and is correspondingly decreased when anion levels are increased. The initial stage of the oxidation of Hb is relatively insensitive to steric alterations and thus reflects, primarily, the electronic aspects of the quaternary (T, T', T", T"'...) <--> equilibrium. We show that the reactivity of the sterically obscured sulfhydryl of beta93 Cys in deoxy Hb is much greater in chloride-free buffers than in buffers with added chloride. Anion-induced decreases in the extent and frequency of conformational fluctuations of subunits within the T-quaternary state thus reduce sulfhydryl reactivity as well as oxygen affinity. This parallel in anionic control of function allowed us to test, and disprove, the possibility that uncompensated positive charges in the central cavity of Hb Deer Lodge increase the frequency and extent of conformational fluctuations in its deoxy structure. This Hb variant exhibits increased anion sensitivity, increased oxygen affinity, and increased ease of oxidation, but without increased reactivity of its sulfhydryl groups, indicating that active-site alterations in deoxy Hb Deer Lodge are primarily electronic and not associated with increased conformational fluctuations within its T state. The restoration of normal properties in Hb Deer Lodge by addition of anions reinforces our conclusion that anionic control can be exerted through both steric and electronic alterations. The anionic control of fluctuations within the T state of Hb illustrates an important principle of macromolecular structure-function relationships: that functional regulation can be achieved by alterations in conformational rigidity.
ARTICULAR REPLACEMENT FOR THE HUMERAL HEAD (1955)

Department of Orthopaedic Surgery, College of Physicians and Surgeons, Columbia University, and the Fracture Service, Presbyterian-New York Orthopaedic Hospitals, New York
Novel Broadband Circularly Polarized Cavity-Backed Aperture Antenna With Traveling Wave Excitation (2009)

A novel broadband circularly polarized aperture antenna is presented that uses traveling-wave excitation as the design concept. The antenna configuration consists of a circular radiating aperture, a backed cavity, and an equiangular tapered strip outer-fed by a microstrip transmission line. Operating with a traveling wave excitation, the proposed antenna contains inherent broadband characteristics in terms of the impedance, axial ratio, and gain performances. The presented antenna is comprehensively investigated, including the working principles, design consideration, and parametric studies. In addition, the research interests are extended to a 2 × 2 antenna array. Promising results from the experimental 2 × 2 array are achieved, including the 10-dB return loss bandwidth of 70%, the 3-dB axial ratio bandwidth of 50%, and the half-power (3-dB) gain bandwidth of 40% with a maximum gain about 11 dBi. The measured and simulated results are well complied with each other.
Neonatal Necrotizing Enterocolitis (1978)

A method of clinical staging for infants with necrotizing enterocolitis (NEC) is proposed. On the basis of assigned stage at the time of diagnosis, 48 infants were treated with graded intervention. For Stage I infants, vigorous diagnostic and supportive measures are appropriate. Stage II infants are treated medically, including parenteral and gavage aminoglycoside antibiotic, and Stage III patients require operation. All Stage I patients survived, and 32 of 38 Stage II and III patients (85%) survived the acute episode of NEC. Bacteriologic evaluation of the gastrointestinal microflora in these neonates has revealed a wide range of enteric organisms including anaerobes. Enteric organisms were cultured from the blood of four infants dying of NEC. Sequential cultures of enteric organisms reveal an alteration of flora during gavage antibiotic therapy. These studies support the use of combination antimicrobial therapy in the treatment of infants with NEC.
Proppant selection for fracturing and sand control (1995)

Starting with definitions of gravel, sand and proppants, this article proceeds to discuss the basic design dilemma of selecting proppant size to achieve the optimum permeability of larger particles vs. higher strength and sand screening ability of smaller sizes. Equations for preventing sand invasion by velocity control are introduced and tables of data give engineers actual design information; tips on table use are included. Hydraulic frac/gravel pack treatments are accepted means of obtaining high well productivity and sand control. A one-step, tip-screenout efficiently creates a short fracture through near-wellbore formation damage and packs the screen/casing annulus to prevent sand production.
3DTouch: A wearable 3D input device for 3D applications (2015)

3D applications appear in every corner of life in the current technology era. There is a need for an ubiquitous 3D input device that works with many different platforms, from head-mounted displays (HMDs) to mobile touch devices, 3DTVs, and even the Cave Automatic Virtual Environments. We present 3DTouch [1], a novel wearable 3D input device worn on the fingertip for 3D manipulation tasks. 3DTouch is designed to fill the missing gap of a 3D input device that is self-contained, mobile, and universally works across various 3D platforms. This video presents a working prototype of our solution, which is described in details in the paper [1]. Our approach relies on a relative positioning technique using an optical laser sensor (OPS) and a 9-DOF inertial measurement unit (IMU). The device employs touch input for the benefits of passive haptic feedback, and movement stability. On the other hand, with touch interaction, 3DTouch is conceptually less fatiguing to use over many hours than 3D spatial input devices. We propose a set of 3D interaction techniques including selection, translation, and rotation using 3DTouch. An evaluation also demonstrates the device's tracking accuracy of 1.10 mm and 2.33 degrees for subtle touch interaction in 3D space. We envision that modular solutions like 3DTouch opens up a whole new design space for interaction techniques to further develop on.
Comparison of Descriptive Sensory Analysis and Chemical Analysis for Oxidative Changes in Milk (2006)

Oxidation in 3 types of bovine milk with different fatty acid profiles obtained through manipulation of feed was evaluated by analytical methods quantifying the content of potential antioxidants, the tendency of formation of free radicals, and the accumulation of primary and secondary oxidation products. The milk samples were evaluated in parallel by descriptive sensory analysis by a trained panel, and the correlation between the chemical analysis and the descriptive sensory analysis was evaluated. The fatty acid composition of the 3 types of milk was found to influence the oxidative and lipolytic changes occurring in the milk during chill storage for 4 d. Sensory analysis and chemical analysis showed high correlation between the typical descriptors for oxidation such as cardboard, metallic taste, and boiled milk and specific chemical markers for oxidation such as hexanal. Notably, primary oxidation products (i.e., lipid hydroperoxides) and even the tendency of formation of radicals as measured by electron spin resonance spectroscopy were also highly correlated to the sensory descriptors for oxidation. Electron spin resonance spectroscopy should accordingly be further explored as a routine method for detection of early events in lipid oxidation in milk to predict shelf-life.
Stimulation of Secretory Antibody Following Oral Administration of Antigen (1988)

IgA antibodies produced by plasma cells in secretory tissues associated with mucosal surfaces represent a major host defense against infectious agents. Precursors of these IgA-producing cells originate in gut-associated lymphoid tissue and, to a lesser extent, in bronchial-associated lymphoid tissue and migrate via the blood not only to gut but also to other mucosal tissues, forming a common mucosal immune system. Oral administration of antigen leads to priming of precursor cells in the gut and subsequent occurrence of specific secretory IgA (S-IgA) antibody in saliva, milk, tears, and the respiratory and genital tracts. On the basis of a review of the world literature, it has been concluded that oral live vaccines elicit higher antibody titers in remote-site secretions and in serum than do oral killed vaccines, which usually stimulate only relatively low levels of local secretory antibody. Oral immunization induces S-IgA in children and adults (including the elderly) without detectable adverse effects. Despite a number of remaining questions, oral immunization against extraintestinal infections is a promising area for future clinical studies.