gebhart/patrepeval huggingface dataset:
Fibrinogen and hemoglobin predict near future cardiovascular events in asymptomatic individuals (2021)

To identify circulating proteins predictive of acute cardiovascular disease events in the general population, we performed a proteomic screen in plasma from asymptomatic individuals. A "Discovery cohort" of 25 individuals who subsequently incurred a cardiovascular event within 3 years (median age = 70 years, 80% male) was matched to 25 controls remaining event-free for > 5 years (median age = 72 years, 80% male). Plasma proteins were assessed by data independent acquisition mass spectrometry (DIA-MS). Associations with cardiovascular events were tested using Cox regression, adjusted for the New Zealand Cardiovascular Risk Score. Concentrations of leading protein candidates were subsequently measured with ELISAs in a larger (n = 151) independent subset. In the Discovery cohort, 76 plasma proteins were robustly quantified by DIA-MS, with 8 independently associated with cardiovascular events. These included (HR = hazard ratio [95% confidence interval] above vs below median): fibrinogen alpha chain (HR = 1.84 [1.19-2.84]); alpha-2-HS-glycoprotein (also called fetuin A) (HR = 1.86 [1.19-2.93]); clusterin isoform 2 (HR = 1.59 [1.06-2.38]); fibrinogen beta chain (HR = 1.55 [1.04-2.30]); hemoglobin subunit beta (HR = 1.49 [1.04-2.15]); complement component C9 (HR = 1.62 [1.01-2.59]), fibronectin isoform 3 (HR = 0.60 [0.37-0.99]); and lipopolysaccharide-binding protein (HR = 1.58 [1.00-2.49]). The proteins for which DIA-MS and ELISA data were correlated, fibrinogen and hemoglobin, were analyzed in an Extended cohort, with broader inclusion criteria and longer time to events, in which these two proteins were not associated with incident cardiovascular events. We have identified eight candidate proteins that may independently predict cardiovascular events occurring within three years in asymptomatic, low-to-moderate risk individuals, although these appear not to predict events beyond three years.
Estimating beauty ratings of videos using supervoxels (2013)

The major low-level perceptual components that influence the beauty ratings of video are color, contrast, and motion. To estimate the beauty ratings of the NHK dataset, we propose to extract these features based on supervoxels, which are a group of pixels that share similar color and spatial information through the temporal domain. Recent beauty methods use frame-level processing for visual features and disregard the spatio-temporal aspect of beauty. In this paper, we explicitly model this property by introducing supervoxel-based visual and motion features. In order to create a beauty estimator, we first identify 60 videos (either beautiful or not beautiful) in the NHK dataset. We then train a neural network regressor using the supervoxel-based features and binary beauty ratings. We rate the 1000 videos in the NHK dataset and rank them according to their ratings. When comparing our rankings with the actual rankings of the NHK dataset, we obtain a Spearman correlation coefficient of 0.42.
CTX-M-Type Extended-Spectrum β-Lactamase That Hydrolyzes Ceftazidime through a Single Amino Acid Substitution in the Omega Loop (2001)

Escherichia coli ILT-1, Klebsiella pneumoniae ILT-2, and K. pneumoniae ILT-3 were isolated in May 1999 in Paris, France, from a rectal swab of a hospitalized 5-month-old girl. These isolates had a clavulanic acid-inhibited substrate profile that included expanded-spectrum cephalosporins. The MICs of cefotaxime were higher for E. coli ILT-1 and K. pneumoniae ILT-2 than for K. pneumoniae ILT-3, while the opposite was found for the MICs of ceftazidime. Genetic and biochemical analyses revealed that E. coli ILT-1 and K. pneumoniae ILT-2 produced the CTX-M-18 beta-lactamase, while K. pneumoniae ILT-3 produced the CTX-M-19 beta-lactamase. The amino acid sequence of the CTX-M-18 beta-lactamase differed from that of the CTX-M-9 beta-lactamase by an Ala-to-Val change at position 231, while CTX-M-19 possessed an additional Pro-to-Ser change at position 167 in the omega loop of Ambler class A enzymes. The latter amino acid substitution may explain the CTX-M-19-mediated hydrolysis of ceftazidime, which has not been reported for other CTX-M-type enzymes. The bla(CTX-M-18) and bla(CTX-M-19) genes were located on transferable plasmids that varied in size (ca. 60 and 50 kb, respectively) but that showed similar restriction patterns.
NOPE: Novel Object Pose Estimation from a Single Image (2023)

The practicality of 3D object pose estimation remains limited for many applications due to the need for prior knowledge of a 3D model and a training period for new objects. To address this limitation, we propose an approach that takes a single image of a new object as input and predicts the relative pose of this object in new images without prior knowledge of the object's 3D model and without requiring training time for new objects and categories. We achieve this by training a model to directly predict discriminative embeddings for viewpoints surrounding the object. This prediction is done using a simple U-Net architecture with attention and conditioned on the desired pose, which yields extremely fast inference. We compare our approach to state-of-the-art methods and show it outperforms them both in terms of accuracy and robustness. Our source code is publicly available at https://github.com/nv-nguyen/nope
Site‐Specifically Arraying Small Molecules or Proteins on DNA Using An Expanded Genetic Alphabet (2013)

A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modification of the amplified DNA by Click chemistry is reported. With the d5SICS scaffold a propynyl ether linker is accommodated better than its aliphatic analogue, but not as well as the protected propargyl amine linker explored previously. It was also found that with the dMMO2 and dDMO analogues, the dMMO2 position para to the glycosidic linkage is best suited for linker attachment and that although aliphatic and ether-based linkers are similarly accommodated, the direct attachment of an ethynyl group to the nucleobase core is most well tolerated. To demonstrate the utility of these analogues, a variety of them were used to site-selectively attach a biotin tag to the amplified DNA. Finally, we use d5SICS(CO) -dNaM to couple one or two proteins to amplified DNA, with the double labeled product visualized by atomic force microscopy. The ability to encode the spatial relationships of arrayed molecules in PCR amplifiable DNA should have important applications, ranging from SELEX with functionalities not naturally present in DNA to the production, and perhaps "evolution" of nanomaterials.
Neutrino-KAVE: An immersive visualization and fitting tool for neutrino physics education (2014)

Water Cherenkov neutrino detectors, like the existing Super-Kamiokande ("Super-K") and the planned Hyper-Kamiokande ("Hyper-K") detectors, are used to study neutrino particle physics. These detectors consist of large vessels holding many thousands of tons of water, as well as tens of thousands of photomultiplier tubes. Such detectors produce large and multi-layered datasets well-suited to immersive visualization and interaction. We have developed a novel virtual reality (VR) application called Neutrino-KAVE which functions as an visualization and data interaction application. Neutrino-KAVE displays the collocation of photon sensors and their color-coded data within a to-scale representation of the Super-K or Hyper-K detector, and provides a new visualization technique for neutrino interaction patterns. Neutrino-KAVE also provides both a mechanism for modifying aspects of the presented data set, and a user interface for system control of this multifaceted application. In this paper, we describe in detail our implementation and design choices. We also report on its use cases, initial reception, and future development.
<Original Article>TDP-43 in the skin of amyotrophic lateral sclerosis patients. (2017)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease. A common characteristic of ALS pathology is cytoplasmic inclusions primarily composed of transactive response DNA-binding protein of 43 kDa (TDP-43). Production of TDP-43 in the central nervous system is strictly regulated, but it is not known whether this is also true in the skin of ALS patients. We found a gradual but significant reduction in epidermal TDP-43 mRNA expression with illness progression in ALS patients with upper-limb onset. However, the immunoblotting analysis revealed more TDP-43 protein in the skin of patients with upper-limb onset than of those with other onsets. There was no correlation between the TDP-43 mRNA expression and protein levels, indicating that the mechanism of TDP-43 autoregulation in the patients' skin gradually failed. ALS diagnosis depends on clinical signs and electrophysiological findings, making early diagnosis difficult. TDP-43, as quantified by immunoblot analysis of biopsied skin, is a potential new biomarker of ALS.
Vibration and Sound-Radiation Analysis for Designing a Low-Noise Gearbox with a Multi-Stage Helical Gear System (2003)

A method for predicting gear noise from the vibration step to the sound-generation step of a complete gear system, including a gearbox, was developed. This method consists of three separate steps: gear-vibration analysis by an in-house program, gearbox-vibration analysis by an FEA program, and sound-radiation analysis by a commercial software. By using this method, it can obtain the vibration behavior of the gear and gearbox, and the distribution of the sound-pressure around the gearbox and identify the areas from which noise radiates intensely. To validate the method, we measured the displacement of a gear shaft, the acceleration of points on the surface of the gearbox, and the sound-pressure levels around the gearbox. The measured results agreed well with the corresponding calculations. According to the calculated noise, a low-noise gearbox was designed by adding ribs near the antinodes of the gearbox's vibration mode.
Extended home use of an advanced osseointegrated prosthetic arm improves function, performance, and control efficiency (2021)

<i>Objective.</i>Full restoration of arm function using a prosthesis remains a grand challenge; however, advances in robotic hardware, surgical interventions, and machine learning are bringing seamless human-machine interfacing closer to reality.<i>Approach.</i>Through extensive data logging over 1 year, we monitored at-home use of the dexterous Modular Prosthetic Limb controlled through pattern recognition of electromyography (EMG) by an individual with a transhumeral amputation, targeted muscle reinnervation, and osseointegration (OI).<i>Main results.</i>Throughout the study, continuous prosthesis usage increased (1% per week,<i>p</i>< 0.001) and functional metrics improved up to 26% on control assessments and 76% on perceived workload evaluations. We observed increases in torque loading on the OI implant (up to 12.5% every month,<i>p</i>< 0.001) and prosthesis control performance (0.5% every month,<i>p</i>< 0.005), indicating enhanced user integration, acceptance, and proficiency. More importantly, the EMG signal magnitude necessary for prosthesis control decreased, up to 34.7% (<i>p</i>< 0.001), over time without degrading performance, demonstrating improved control efficiency with a machine learning-based myoelectric pattern recognition algorithm. The participant controlled the prosthesis up to one month without updating the pattern recognition algorithm. The participant customized prosthesis movements to perform specific tasks, such as individual finger control for piano playing and hand gestures for communication, which likely contributed to continued usage.<i>Significance.</i>This work demonstrates, in a single participant, the functional benefit of unconstrained use of a highly anthropomorphic prosthetic limb over an extended period. While hurdles remain for widespread use, including device reliability, results replication, and technical maturity beyond a prototype, this study offers insight as an example of the impact of advanced prosthesis technology for rehabilitation outside the laboratory.
Quantifying Postural Instability with Pose Estimation Software and 3D Depth Extraction (2021)

Abstract Patients who suffer from Parkinson’s Disease are more prone to postural instability, a major risk factor for falls. One of the most common clinical methods of gauging the severity of a patient’s postural instability is with the retropulsion test [1], in which a clinician perturbs the balance of the patient and then rates their response to the perturbation. This test is subjective and largely based on the observations made by the clinician. In order to improve postural instability diagnosis and encourage more meaningful therapies for this cognitive-motor symptom, there is a clinical need to enable more objective, quantifiable approaches to measuring postural instability. In this paper, we describe a novel computational approach to quantifying the number, length, and trajectory of steps taken during a retropulsion test or other type of balance perturbation from a single camera facing the anterior side (front) of the subject. The computational framework involved first analyzing the video data using markerless pose estimation algorithms to track the movement of the subject’s feet. These pixel data were then converted from 2D to 3D using calibrated transformation functions, and then analyzed for consistency when compared to the known step lengths. The testing data showed accurate step length estimation within 1 cm, which suggests this computational approach could have utility in a variety of clinical environments.
Visual Data Mining of Brain Cells (2002)

Little is known about the influence of morphological variablity on the physiological response of brain cells. It is assumed that variables such as the number of branching points in the cell tree-like structure, its area and the change in shape from soma to terminals may influence the neuron behavior differently under different electric stimulation. In laboratory experiments, it is difficult to separate the electrophysiological effects of biochemical differences (i. e., channel types and their distributions) from those of the morphological differences in a neuron&amp;apos;s behavior. Therefore, wehaveused computer simulations of 3D neuroanatomical data of hippocampal cells while keeping the electrophysiological model constant across different neurons. This allowed us to look specifically at the morphological influence on the neuronal function. We have obtained neuroanatomical data (particularly, hippocampal pyramidal cells) from public electronic archives. Because of the amount of painstaking work to reconstruct the three-dimemsional structure of a neuron, these archives tend to be very small (ranging from 3 to 50 cells). Additionally, there is the possibility that different archives have significant morphological differences due to the reconstruction technique. Therefore, it is difficult to reach robust conclusions on the relationship between morphological parameters and electrophysiological output. However, we found that visual data mining techniques combined with computational neural modeling is a very effective wayto detect some structure in the data. There are, indeed, morphological variables that can be used to determine whether hippocampal pyramidal cells spike, burst, or have a plateau in response to a given level of input current.
Use of a Novel Pressure Distribution System for Severely Ill Neonates: A Clinical Pilot Study Carried out by the PREPICare Consortium (2022)

Abstract Background : Pressure Injuries are not exclusively an adult phenomenon; various risk factors contribute to a high prevalence rate of 43% in the neonatal and pediatric intensive care population. Effective preventive measures in this population are limited. Methods : We performed a pilot study to analyze the distribution and localization of support surface interface pressures in neonates in a pediatric intensive care unit (PICU). The hypothesis was that pressure redistribution by a novel air mattress would reduce pressure peaks in critical neonates. The measurements were conducted in a 27-bed level III PICU between November and December 2020. This included measuring pressure distribution and pressure peaks for five neonates positioned on either a state-of-the-art foam mattress or a new prototype air mattress. Results : We confirmed that the pressure peaks were significantly reduced using the prototype air mattress, compared with the state-of-the-art foam mattress. The reduction of mean pressure values was 9%–29%, while the reduction of the highest 10% of pressure values was 23%–41%. Conclusions : The journey to an effective, optimal, and approved product for severely ill neonates to reduce Pressure Injuries is challenging. However, a crucial step was completed by this pilot study with the first pressure measurements in a real-world setting and the successful realization of a decrease in pressure peaks obtained using a prototype air mattress.
Multiplicative complements I (2022)

In this paper, we study how dense a multiplicative basis of order $h$ for $\mathbb{Z}^+\!$ can be, improving on earlier results. Upon introducing the notion of a \textit{multiplicative complement}, we present some tight density bounds.
Analysis of the CHK2 Gene in Lymphoid Malignancies (2001)

The CHK2 gene encodes a protein kinase that is important for the regulation of cell cycle arrest after DNA damage. CHK2 acts downstream of ataxia teleangiecstasia mutated (ATM), modulates the function of p53 and may help mediate cell cycle arrest at G2/M by phosphorylation of Cdc25C. Recently, the human homolog of the checkpoint kinase Cds1 (CHK2) has been suggested to be a tumor suppressor gene. Heterozygous germline mutations have been reported in Li-Fraumeni syndrome (LFS), a highly penetrant familial cancer phenotype, and in sporadic colon cancer. LFS is associated with the development of lymphoid malignancies, especially childhood ALL. Therefore, we analyzed the DNA from 143 lymphoid malignancies to determine whether they had mutations of the CHK2 gene. The 14 exons of CHK2 were studied by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) and sequencing of aberrantly migrating bands. One missense mutation changing serine to phenylalanine (codon 428) in an evolutionarily highly conserved domain was found in a non-Hodgkin's aggressive lymphoma. Another point mutation in the non-coding region was identified in one of adult T-cell leukemias (ATL) samples. This result suggests that mutation of the CHK2 gene may rarely be involved in the development of selected lymphomas.
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution (2015)

DNA methylation pattern mapping is heavily studied in normal and diseased tissues. A variety of methods have been established to interrogate the cytosine methylation patterns in cells. Reduced representation of whole genome bisulfite sequencing was developed to detect quantitative base pair resolution cytosine methylation patterns at GC-rich genomic loci. This is accomplished by combining the use of a restriction enzyme followed by bisulfite conversion. Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) increases the biologically relevant genomic loci covered and has been used to profile cytosine methylation in DNA from human, mouse and other organisms. ERRBS initiates with restriction enzyme digestion of DNA to generate low molecular weight fragments for use in library preparation. These fragments are subjected to standard library construction for next generation sequencing. Bisulfite conversion of unmethylated cytosines prior to the final amplification step allows for quantitative base resolution of cytosine methylation levels in covered genomic loci. The protocol can be completed within four days. Despite low complexity in the first three bases sequenced, ERRBS libraries yield high quality data when using a designated sequencing control lane. Mapping and bioinformatics analysis is then performed and yields data that can be easily integrated with a variety of genome-wide platforms. ERRBS can utilize small input material quantities making it feasible to process human clinical samples and applicable in a range of research applications. The video produced demonstrates critical steps of the ERRBS protocol.
The Structure of the Cyclodextrin Complex. XI. Crystal Structure of Hexakis(2,3,6-tri-<i>O</i>-methyl)-α-cyclodextrin–<i>p</i>-Iodoaniline Monohydrate (1982)

Abstract The crystal structure of hexakis(2,3,6-tri-O-methyl)-α-cyclodextrin–p-iodoaniline complex, C54H96O30·C6H6NI·H2O, was determined by the X-ray method. The crystal is monoclinic with the space group P21, Z=2, a=11.440(4), b=23.674(6), c=13.531(3) Å, and β=91.90(2)°. The structure was solved by the heavy atom method combined with the rigid-body least-squares technique and refined by the block-diagonal least-squares method to the final R-value of 0.11 for 2186 reflections (sinθ⁄λ&amp;lt;0.49). Hexakis(2,3,6-tri-O-methyl)-α-cyclodextrin is in the shape of a truncated elliptical cone; these cones are stacked along the a axis to form a channel-type structure. The guest p-iodoaniline and water molecules are located in the channel. The iodophenyl group is inserted rather loosely from the base side of the truncated cone. The iodine atom is located at the center of the cavity, while the amino group outside the host cavity forms a hydrogen bond with the water molecule. The water molecule is also hydrogen bonded to the adjacent host molecule along the channel. The crystal is built up of columns of the host molecules, which are closely packed in the van der Waals contact.
Anatomical double‐bundle anterior cruciate ligament reconstruction moderately improved tegner scores over the long‐term: a systematic review and meta‐analysis of randomized controlled trials (2022)

I.
Loss of R2D2 Proteins ROPN1 and ROPN1L Causes Defects in Murine Sperm Motility, Phosphorylation, and Fibrous Sheath Integrity1 (2013)

The fibrous sheath (FS) is a flagellar cytoskeletal structure unique to sperm that surrounds the outer dense fibers and axoneme. Its primary components are A-kinase anchoring proteins (AKAPs) 3 and 4, which suggests that the FS affects flagellar beating via the scaffolding of signaling pathways necessary for motility. Sperm proteins ROPN1 and ROPN1L bind AKAP3. To determine the role of ROPN1 and ROPN1L in sperm function, we created mice deficient in ROPN1 (RKO), mice deficient in ROPN1L (RLKO), and double knockout mice (DKO). All three strains of mice had normal testicular morphology and spermatogenesis. Only the DKOs had obvious defects in sperm morphology (thinning and shredding of the principal piece), which was accompanied by a reduction in AKAP3 levels. RLKO mice had slightly reduced sperm motility and increased levels of ROPN1. RKO mice had moderately impaired motility and increased levels of ROPN1L. DKO sperm were immotile. We have previously determined that RKO male mice are subfertile, and DKO males are infertile. Together these data indicate that ROPN1L and ROPN1 compensate for each other in the absence of the opposing protein, possibly to maintain AKAP3 incorporation in the FS. Sperm from mice lacking ROPN1L exhibited reductions in both cAMP-dependent protein kinase (PKA) phosphorylation of a 270-kDa protein (perhaps FSCB), and in capacitation-induced tyrosine phosphorylation. Sperm from mice lacking ROPN1 had reduced levels of FSCB and increased tyrosine phosphorylation of noncapacitated sperm. These data demonstrate that mutations in ROPN1 and ROPN1L can cause defects in FS integrity, sperm motility, and PKA-dependent signaling processes, leading to male infertility.