gebhart/patrepeval huggingface dataset:
Learning-based solution to phase error correction in T2*-weighted GRE scans (2018)

Long-TE gradient recalled-echo (GRE) scans are prone to phase artifacts due to B0 inhomogeneity. We propose a learning-based approach that does not rely on navigator readouts and allows to infer phase error offsets directly from corrupted data. Our method does not need to be pre-trained on a database of medical images that match a contrast/acquisition protocol of the input image. A sufficient input is a raw multi-coil spectrum of the image that needs to be corrected. We train a convolutional neural network to predict phase offsets for each k-space line of a 2D image. We synthesize training examples online by reconvolving the corrupted spectrum with point spread functions (PSFs) of the coil sensitivity profiles and superimposing artificial phase errors, which we attempt to predict. We evaluate our approach on “in vivo” data acquired with GRE sequence, and demonstrate an improvement in image quality after phase error correction.
Supplementary Data from Novel Radiomic Measurements of Tumor-Associated Vasculature Morphology on Clinical Imaging as a Biomarker of Treatment Response in Multiple Cancers (2023)

Supplementary Data from Novel Radiomic Measurements of Tumor-Associated Vasculature Morphology on Clinical Imaging as a Biomarker of Treatment Response in Multiple Cancers
Detecting Intra-enterprise Scanning Worms based on Address Resolution (2006)

Signature-based schemes for detecting Internet worms often fail on zero-day worms, and their ability to rapidly react to new threats is typically limited by the requirement of some form of human involvement to formulate updated attack signatures. We propose an anomaly-based detection technique detailing a method to detect propagation of scanning worms within individual network cells, thus protecting internal networks from infection by internal clients. Our software implementation indicates that this technique is both accurate and rapid enough to enable automatic containment and suppression of worm propagation within a network cell. Our approach relies on an aggregate anomaly score, derived from the correlation of address resolution protocol (ARP) activity from individual network attached devices. Our preliminary analysis and prototype indicate that this technique can be used to rapidly detect zero-day worms within a very small number of scans
Global Diversity within and between Human Herpesvirus 1 and 2 Glycoproteins (2015)

Human herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are large DNA viruses associated with recurring oral or genital erosions that transmit virus. Up to 12 HSV-1 and HSV-2 glycoproteins are involved in HSV cell entry or are required for viral spread in animals, albeit some are dispensable for replication in vitro. The recent availability of comparable numbers of full-length HSV-1 and HSV-2 sequences enabled comparative analysis of gene diversity of glycoproteins within and between HSV types. Overall, we found less glycoprotein sequence diversity within HSV-2 than within the HSV-1 strains studied, while at the same time, several HSV-2 glycoproteins were evolving under less selective pressure. Because HSV glycoproteins are the focus of antibody tests to detect and differentiate between infections with the two strains and are constituents of vaccines in clinical-stage development, these findings will aid in refining the targets for diagnostic tests and vaccines.
CORR Insights®: Prevalence of Triangular Fibrocartilage Complex Abnormalities Regardless of Symptoms Rise With Age: Systematic Review and Pooled Analysis (2014)

C han and colleagues have attempted to ask a relevant clinical question regarding the evaluation of triangular fibrocartilage complex lesions (TFCC) of the wrist: What relationships exist between TFCC tears, age, and pain? All too often we have patients who have been referred to us for wrist pain and have been diagnosed as having a ‘‘tear’’ involving the TFCC. Moreover, patients may or may not have a history of a traumatic event precipitating the pain. Unfortunately, our diagnostic evaluation of ulnar-sided wrist pain has not changed substantially for several decades now. We know from our experience in other orthopaedic clinical problems that the simple presence of a radiographic finding does not necessarily mean that the finding is generating the pain. Patients with low-back pain often have radiographic findings that are not clinically relevant. SLAP lesions of the shoulder, likewise, often are asymptomatic, coincidental findings were noted on MRIs in the workup of shoulder pain.
ChemInform Abstract: DIRECT SYNTHESIS USING VANADIUM ATOMS, 3. BINARY CARBONYLS OF VANADIUM, V(CO)N (WHERE N = 1‐5) (1977)

Abstract Die IR‐spektroskopischen Daten für die durch Kokondensation von V‐Atomen mit CO in verdünnter Edelgasmatrix bei 6‐10 Ksynthetisierten Titelcarbonyle werden mitgeteilt.
An interventriculo‐septal ganglion mediates the vagal postganglionic control of contractility of the right ventricle of the cat heart (2008)

We investigated the role of the interventriculo‐septal (IVS) ganglion as a potential source of vagal postganglionic control of right ventricular contractility. Prior evidence demonstrated that this ganglion provides a major source of vagal postganglionic innervation to both right and left ventricles. Blockade of the IVS ganglion with hexamethonium significantly reduced the vagally‐induced changes in right ventricular contractility in the short (transverse) and long (longitudinal) axis, without affecting heart rate or blood pressure responses to left vagal stimulation. The central pathway controlling the IVS ganglion was investigated by neuroanatomical methods. The retrograde tracer, cholera toxin‐β subunit conjugated with horseradish peroxidase (CTB‐HRP) was injected into the region of the IVS ganglion and retrogradely labeled cells were found exclusively in the ventrolateral nucleus ambiguus (NA‐VL) with the greatest concentration at the level of the area postrema. These data indicate that the IVS exerts a predominant role in modulation of RV contractile function, and that its major pre‐ganglionic input arises from the left NA‐VL. This research was supported in part by NIH‐NIGMCS 2S06GM008016 to MDG, NIH‐NINDS‐SNRP 2 U54 NS039407 to MDG and VJM, NIH‐NIMH 1 R24MH067627 to MDG and VJM, 2 G12 RR003048 from the RCMI Program to MDG and NIH‐HL71830 to JLA.
Large-Area Chemical and Biological Decontamination Using a High Energy Arc Lamp (HEAL) System. (2008)

Methods for quickly decontaminating large areas exposed to chemical and biological (CB) warfare agents can present significant logistical, manpower, and waste management challenges. Oak Ridge National Laboratory (ORNL) is pursuing an alternate method to decompose CB agents without the use of toxic chemicals or other potentially harmful substances. This process uses a high energy arc lamp (HEAL) system to photochemically decompose CB agents over large areas (12 m2). Preliminary tests indicate that more than 5 decades (99.999%) of an Anthrax spore simulant (Bacillus globigii) were killed in less than 7 seconds of exposure to the HEAL system. When combined with a catalyst material (TiO2) the HEAL system was also effective against a chemical agent simulant, diisopropyl methyl phosphonate (DIMP). These results demonstrate the feasibility of a rapid, large-area chemical and biological decontamination method that does not require toxic or corrosive reagents or generate hazardous wastes.
A comparison of channel estimation techniques in OFDM with a proposed improvement in FFT based estimator (2009)

In this paper, we compare the performance of several channel estimation techniques in training and pilot based OFDM systems. Both sample and non sample spaced channels have been considered along with null sub-carriers. We also present a modified interpolation based FFT estimator for training based channel estimation in presence of null sub-carriers for sample spaced channels. Improvement in performance compared to conventional FFT based estimator is shown through simulation results.
High-Throughput Random Access Using Successive Interference Cancellation in a Tree Algorithm (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Random access is well motivated and has been widely applied when the network traffic is bursty and the expected throughput is not high. The main reason behind relatively low-throughput expectations is that collided packets are typically discarded. In this paper, we develop a novel protocol exploiting successive interference cancellation (SIC) in a tree algorithm (TA), where collided packets are reserved for reuse. Our SICTA protocol can achieve markedly higher maximum stable throughput relative to existing alternatives. Throughput performance is analyzed for general <emphasis><formula formulatype="inline"> <tex>$d$</tex></formula></emphasis>-ary SICTA with both gated and window access. It is shown that the throughput for <emphasis><formula formulatype="inline"> <tex>$d$</tex></formula></emphasis>-ary SICTA with gated access is about <emphasis><formula formulatype="inline"><tex>$(\ln d)/(d-1)$</tex></formula></emphasis>, and can reach <emphasis><formula><tex>$0.693$</tex></formula></emphasis> for <emphasis><formula formulatype="inline"><tex>$d=2$</tex></formula></emphasis>. This represents a 40% increase over the renowned first-come-first-serve (FCFS) <emphasis><formula> <tex>$0.487$</tex></formula></emphasis> tree algorithm. Delay performance is also analyzed for SICTA with gated access, and numerical results are provided. </para>
Layered GaTe crystals for radiation detectors (2010)

In this work we investigated a new method of growing detector grade large GaTe layered chalcogenide single crystals. GaTe ingots (2" diameter) were grown by a novel method using graphite crucible by slow crystallization from a melt of high purity (7N) Ga and Te precursors in an argon atmosphere. GaTe samples from the monocrystalline area of the ingot have been cleaved mechanically and characterized using x-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive analysis by x-rays (EDAX), atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS), transmission line matrix method (TLM), resistivity measurements using van der Pauw technique, Hall Effect, and Capacitance-Voltage measurements. Our investigations reveal high potential for developing superior quality GaTe crystals using this growth technique for growing large volume inexpensive GaTe single crystals for nuclear radiation detectors.
Posterior fossa stereotaxic biopsy using the Brown-Roberts-Wells stereotaxic system (1989)

Stereotaxic biopsy has been shown to be a reliable means of diagnosing posterior fossa lesions. The authors describe a technique for infratentorial transcerebellar stereotaxic access to posterior fossa parenchymal lesions using the Brown-Roberts-Wells apparatus in its standard commercial configuration. The necessity for tissue diagnosis of these lesions is briefly discussed.
Vitamin D receptor FokI polymorphism and the risks of colorectal cancer, inflammatory bowel disease, and colorectal adenoma (2018)

Based on an inverse association between vitamin D levels and the risks of colorectal diseases, a functional start codon polymorphism in the vitamin D receptor (VDR) gene is speculated to affect the risks for these diseases. To validate this hypothesis, we first conducted a case-control study of 695 colorectal cancer patients and 1,397 controls. The association of VDR FokI polymorphism with colorectal cancer risk was analyzed using a logistic regression model. In the present case-control study, compared to the F allele, the f allele seemed to be associated with lower risks of colon cancer and advanced colorectal cancer. Additionally, a meta-analysis of 27 studies was conducted to combine findings from previous studies investigating the association of FokI polymorphism with colorectal disease using a random effects model. In the present meta-analysis, the f allele was positively associated with the risk of inflammatory bowel disease, including Crohn's disease and ulcerative colitis. However, this allele was inversely associated with colon cancer and was not associated with the risk of rectal cancer or colorectal adenoma. In conclusion, the findings from this study imply that the role of VDR FokI polymorphism may differ based on the type and severity of colorectal disease.
Novel Ribosomal Mutations in Staphylococcus aureus Strains Identified through Selection with the Oxazolidinones Linezolid and Torezolid (TR-700) (2009)

TR-700 (torezolid), the active moiety of the novel oxazolidinone phosphate prodrug TR-701, is highly potent against gram-positive pathogens, including strains resistant to linezolid (LZD). Here we investigated the potential of Staphylococcus aureus strains ATCC 29213 (methicillin-susceptible S. aureus [MSSA]) and ATCC 33591 (methicillin-resistant S. aureus [MRSA]) to develop resistance to TR-700. The spontaneous frequencies of mutation of MSSA 29213 and MRSA 33591 resulting in reduced susceptibility to TR-700 at 2 x the MIC were 1.1 x 10(-10) and 1.9 x 10(-10), respectively. These values are approximately 16-fold lower than the corresponding LZD spontaneous mutation frequencies of both strains. Following 30 serial passages in the presence of TR-700, the MIC for MSSA 29213 remained constant (0.5 microg/ml) while increasing eightfold (0.25 to 2.0 microg/ml) for MRSA 33591. Serial passage of MSSA 29213 and MRSA 33591 in LZD resulted in 64- and 32-fold increases in LZD resistance (2 to 128 microg/ml and 1 to 32 microg/ml, respectively). Domain V 23S rRNA gene mutations (Escherichia coli numbering) found in TR-700-selected mutants included T2500A and a novel coupled T2571C/G2576T mutation, while LZD-selected mutants included G2447T, T2500A, and G2576T. We also identified mutations correlating with decreased susceptibility to TR-700 and LZD in the rplC and rplD genes, encoding the 50S ribosomal proteins L3 and L4, respectively. L3 mutations included Gly152Asp, Gly155Arg, Gly155Arg/Met169Leu, and DeltaPhe127-His146. The only L4 mutation detected was Lys68Gln. TR-700 maintained a fourfold or greater potency advantage over LZD against all strains with ribosomal mutations. These data bring to light a variety of novel and less-characterized mutations associated with S. aureus resistance to oxazolidinones and demonstrate the low resistance potential of torezolid.
Thermal and optical characterization of resonant coupling between surface plasmon polariton and semiconductor waveguides (2011)

Resonant coupling between an Au-InP surface plasmon polariton (SPP) and an InP/InGaAsP ridge waveguide is investigated. The general design requirements for evanescent coupling between a low-loss waveguide and a highly absorptive SPP are described, and experimental results are presented for fabricated devices. Coupling from the ridge to the SPP is confirmed using fiber-to-fiber optical power measurements, and thermoreflectance imaging is used to directly measure power coupled to the SPP along the length of the metal waveguide. The role of the thin native oxide at the Au-InP interface is also explored and found to have a significant impact on coupling.
Association of Morbidity with Extent of Resection and Cavernous Sinus Invasion in Sphenoid Wing Meningiomas (2011)

See also: Association of Morbidity with Extent of Resection and Cavernous Sinus Invasion in Sphenoid Wing MeningiomasJ Neurol Surg B Skull Base 2012; 73(01): 076-083DOI: 10.1055/s-0032-1304562
Highly reliable vertical NAND technology with biconcave shaped storage layer and leakage controllable offset structure (2010)

The performance and reliability of 3-D NAND cells fabricated by TCAT (Terabit Cell Array Transistor) technology have been improved significantly via a damascened metal gates and a controlled offset between BL contact and select transistor. The damascened metal gate providing sufficiently low resistance is achieved by adopting a novel metal process. Highly suppressed disturbance property is achieved by the appropriate offset which reduces the leakage current through the select transistor. It is proved that the TCAT NAND is a manufacturable technology in terms of reliability as well as performance in a channel hole with a diameter of 90nm.
Aging and Cancer Vaccines (2013)

Cancer vaccination is less effective at old than at young age, due to T cell unresponsiveness. This is caused by age-related changes of the immune system. Major immune defects at older age are lack of naive T cells, impaired activation pathways of T cells and antigen-presenting cells (APC), and age-related changes in the tumor microenvironment (TME). Also innate immune responses are affected by aging, but this seems less abundant than adaptive immune responses. In this review we compared various cancer vaccine studies at young and old age, demonstrating the importance of both innate and adaptive immune responses for cancer immunotherapy. Moreover, we found suggestive evidence that innate immune responses could help improve adaptive immune responses through cancer vaccination in old age.
ChemInform Abstract: Study of the Influence of Ultrasound and Aqueous Solvent on the Diels‐Alder Reaction: The Case of Cyclopentadiene and Acetamidoacrylates. (1989)

Abstract The cycloaddition reaction of the acetamidoacrylates (II) or (V) with excess cyclopentadiene, yielding the norbornenecarboxylates (III) and (IV) or (VI) and (VII), is performed in toluene or water without or with ultrasonic irradiation.
Fabrication and characterization of L1/sub 0/ FePt nanoparticles (2005)

Discontinuous FePt films with thicknesses raging from 0.25 nm to 2 nm were prepared by co-sputtering using high vacuum dc magnetron sputtering. Ex-situ anneals in one atmosphere of a flowing reducing gas, argon with 3% hydrogen, were used to stabilize the isolated cluster morphology and to induce ordering. Composition ratios were confirmed with RBS and extensive characterization of the nanoparticles was done with transmission electron microscopy (TEM). The particle was found to depend on the annealing temperature and thickness. For 0.25 nm deposition, the typical particle size increases from 2.5 nm to 5 nm with annealing temperature increasing from 500/spl deg/C to 800/spl deg/C For the thickest films of 2 nm deposition, particle size increased from 5.5 nm to 10 nm with increasing annealing temperature.
Association between Severity of Asthma and Degree of Chronic Rhinosinusitis (2011)

Increasing severity of asthma is associated with advancing radiological severity of CRS and a greater prevalence of allergic sensitization and nasal polyposis. This large adult series shows that asthma severity may have a significant correlation with the presentation of CRS. This study adds to the growing support for the unified airway theory.
Prehabilitation prior to kidney transplantation: Results from a pilot study (2018)

Prehabilitation is the process of enhancing preoperative functional capacity to improve tolerance for the upcoming stressor; it was associated with improved postoperative outcomes in a handful of studies, but never evaluated in transplantation. Kidney transplant (KT) candidates may be uniquely suited for prehabilitation because they experience a profound loss of functional capacity while waiting years on dialysis. To better understand the feasibility and effectiveness of prehabilitation in KT, we conducted a pilot study of center-based prehabilitation for candidates; this intervention consisted of weekly physical therapy sessions at an outpatient center with at-home exercises. We enrolled 24 participants; 18 participated in prehabilitation (75% of enrolled; 17% of eligible). 61% were male, 72% were African American, and mean age = 52 (SD = 12.9); 71% of participants had lower-extremity impairment, and 31% were frail. By 2 months of prehabilitation, participants improved their physical activity by 64% (P = 0.004) based on accelerometry. Participants reported high satisfaction. Among 5 prehabilitation participants who received KT during the study, length of stay was shorter than for age-, sex-, and race-matched control (5 vs 10 days; RR = 0.69; 95% CI:0.50-0.94; P = 0.02). These pilot study findings suggest that prehabilitation is feasible in pretransplant patients and may potentially be a strategy to improve post-KT outcomes.
P4‐305: Allosteric potentiation of the M1 muscarinic receptor provides unprecedented selectivity and a novel therapeutic strategy for the treatment of Alzheimer's disease (2008)

Alzheimer's disease (AD) patients suffer from an inexorable loss of cognitive function due in part to the degeneration of the basal forebrain cholinergic projection neurons. Restoring signalling through the post-synaptic muscarinic acetylcholine receptors that mediate cholinergic signalling is thus a promising therapeutic strategy for the symptomatic management of AD. Moreover muscarinic receptor agonists reduce Aβ42 in animal models, suggesting that this class of compounds could address the underlying disease pathology. Unfortunately, multiple non-selective muscarinic receptor agonists have been tested in AD patients and were not tolerated due to unwanted peripheral cholinergic stimulation. Improved selectivity for M1, the most prominently expressed post-synaptic muscarinic receptor in the cortex and hippocampus, could address these tolerability issues, however the high conservation of the acetylcholine binding site between receptor subtypes has precluded the discovery of selective agonists. To achieve selectivity for M1 by discovering and exploiting an allosteric ligand binding site. We screened a chemical library for positive allosteric modulators of the M1 receptor and assessed chemical leads for selectivity in vitro and efficacy in rodent AD models in vivo. We identified Benzyl Quinolone Carboxylic Acid (BQCA), a small molecule potentiator selective for M1. In CHO cells expressing recombinant human receptor, BQCA sensitizes M1 to acetylcholine 83.9-fold (inflection point = 449 nM), while having no potentiation, agonist, or antagonist effect on M2, M3, or M4 receptors up to 100 μM. In the mouse contextual fear conditioning model of episodic-like memory, BQCA fully reversed the cognitive impairment caused by the non-selective muscarinic antagonist scopolamine, demonstrating a critical role for M1 in this type of memory. Importantly BQCA does not show signs of unwanted peripheral cholinergic stimulation at doses that produce central physiological responses. In vivo BQCA and other muscarinic agonists can specifically reduce cortical Aβ42 in some experiments. However, this effect is likely complex and indirect, since it does not occur in cultured neurons and is not consistently observed across species and disease models. BQCA is a highly selective pharmacological reagent for understanding the normal physiology of the M1 receptor and its potential as a therapeutic target for AD.