gebhart/patrepeval huggingface dataset:
p-type doping of MoS2 thin films using Nb (2014)

We report on the first demonstration of p-type doping in large area few-layer films of (0001)-oriented chemical vapor deposited MoS2. Niobium was found to act as an efficient acceptor up to relatively high density in MoS2 films. For a hole density of 3.1 × 1020 cm−3, Hall mobility of 8.5 cm2 V−1 s−1 was determined, which matches well with the theoretically expected values. X-ray diffraction scans and Raman characterization indicated that the film had good out-of-plane crystalline quality. Absorption measurements showed that the doped sample had similar characteristics to high-quality undoped samples, with a clear absorption edge at 1.8 eV. Scanning transmission electron microscope imaging showed ordered crystalline nature of the Nb-doped MoS2 layers stacked in the [0001] direction. This demonstration of substitutional p-doping in large area epitaxial MoS2 could help in realizing a wide variety of electrical and opto-electronic devices based on layered metal dichalcogenides.
Technical engine for democratization of modeling, simulations, and predictions (2012)

Computational science and engineering play a critical role in advancing both research and daily-life challenges across almost every discipline. As a society, we apply search engines, social media, and selected aspects of engineering to improve personal and professional growth. Recently, leveraging such aspects as behavioral model analysis, simulation, big data extraction, and human computation is gaining momentum. The nexus of the above facilitates mass-scale users in receiving awareness about the surrounding and themselves. In this paper, an online platform for modeling and simulation (M&S) on demand is proposed. It allows an average technologist to capitalize on any acquired information and its analysis based on scientifically-founded predictions and extrapolations. The overall objective is achieved by leveraging open innovation in the form of crowd-sourcing along with clearly defined technical methodologies and social-network-based processes. The platform aims at connecting users, developers, researchers, passionate citizens, and scientists in a professional network and opens the door to collaborative and multidisciplinary innovations. An example of a domain-specific model of a pick and place machine illustrates how to employ the platform for technical innovation and collaboration.
Solar models and electron screening (2001)

We investigate the sensitivity of the solar model to changes in the nuclear reaction screening factors. We show that the sound speed profile as determined by helioseismology certainly rules out changes in the screening factors exceeding more than 10% . A slightly improved solar model could be obtained by enhancing screening by about 5% over the Salpeter value. We also discuss how envelope properties of the Sun depend on screening, too. We conclude that the solar model can be used to help settling the on-going dispute about the "correct"screening factors.
Measurement of Transcutaneous Hemoglobin Concentration by Noninvasive White-Light Spectroscopy in Infants (2005)

This pilot study could illustrate a good relation between the 2 methods for measuring hemoglobin. Larger studies are required to validate the spectroscopic method in those with conditions that affect the skin microcirculation (eg, septicemia).
Isolation and structure of huyman carbonic anhydrase II cDNA (1987)

The carbonic anhydrases (CA) represent a multigene family comprising at least five loci. While screening a human liver cDNA library two recombinants containing overlapping CA II cDNA sequences were characterized. EcoR1 fragments were sublconed into pBSM13 and sequenced by the dideoxy chain termination method. The 5' region, corresponding to exons 1 and 2, matched sequences from a human CA II genomic clone. The protein sequence encoded by the cDNAs matched that determined directly. Optimal alignment of the human and, previously reported, mouse CA II cDNAs revealed unexpectedly few nucleotide replacements in the 664 bp shared in the 3' untranslated region. Division of this region into eight 83 bp blocks reveals the following identities: (5')-55%-71%-47%-66%-70%-82%-84%-87%-(3'). The 777 bp translated region shows 80% interspecies identify; 42% of the nucleotide replacements cause amino acid substitutions. The 3' untranslated region of the human CA II cDNA has four potential poly A addition signals; use of these would result in mRNAs of approx. 1.65 (the mRNA cloned), 1.3, 1.1 and 1.0 kb.
DOP26 COVID-19 vaccine effectiveness in Inflammatory Bowel Disease patients on tumor-necrosis factor inhibitors: Real world data from a mass-vaccination campaign (2022)

Abstract Background Some studies have shown decreased serological response to vaccination in patients on anti-tumor necrosis factor (TNF) medications. While the large majority of these patients do seroconvert after vaccination, titers have generally been lower and one study showed reduced neutralizing and inhibitory functions. One real-world population-based study compared found no increased infection rate in anti-TNF treated patients, but infection rates were low. The low event rate mandates exploration in longer-term population-based data. We used the epi-Israeli IBD Research Nucleus (IIRN) database to explore the effectiveness of COVID-19 vaccination in IBD patients in Israel. Methods We included all IBD patients insured in two of the four Israeli HMOs, covering 35% of the population, by validated algorithms, and selected those who received two doses of Pfizer BNT162b2 vaccine. These were matched by date of vaccination ±3 days and demographic variables to non-IBD controls. The primary outcome was incidence of positive COVID-19 PCR following vaccination between December, 2020 to June, 2021. Results 12,640 IBD patients received two vaccine doses; the matched cohort included 4,946 matched pairs (total 9,892 subjects). Mean age was 50.5±16.1 years and median follow-up was 22 weeks (range 4.1–24.4). Fifteen (0.3%) vaccinated IBD patients tested positive compared with 15 (0.3%) vaccinated non-IBD controls (OR=1 [95%CI 0.49–2.05], p=1.0). Patients on anti-TNF and/or corticosteroids did not have a higher incidence of positivity – neither compared to the entire group nor to IBD patients treated with vedolizumab/ustekinumab, even after precise matching for demographics, underlying diseases and IBD severity. Conclusion In a large population-based cohort of IBD patients in Israel, vaccine effectiveness was equivalent to non-IBD controls and was not influenced by treatment with anti-TNF or corticosteroids. Notwithstanding previous findings of impaired serological response in anti-TNF treated IBD patients, this real-world large-scale study shows that vaccine protection is robust in IBD patients, including those on immunosuppressive medications.
Newly discovered naturally occurring organohalogens (2018)

Last year more than 200 naturally occurring organohalogens were described for the first time. These natural products were isolated and characterized from marine algae, sponges, corals, tunicates, bryozoans, marine and terrestrial fungi and bacteria, cyanobacteria, terrestrial plants, slime molds, red ants, and interstellar space. The following examples are illustrative of the extraordinary synthetic virtuosity of nature.
A Survey of Lightweight-Cryptography Implementations (2007)

The tight cost and implementation constraints of high-volume products, including secure RFID tags and smart cards, require specialized cryptographic implementations. The authors review recent developments in this area for symmetric and asymmetric ciphers, targeting embedded hardware and software. In this article, we present a selection of recently published lightweight-cryptography implementations and compare them to state-of-the-art results in their field.
Ultrathin (5-35 nm) SiCNH Dielectrics for Damascene Cu Cap Application: Thickness Scaling and Oxidation Barrier Performance Limitation (2010)

The scaling limit of plasma enhanced chemical vapor deposited (PECVD) ultrathin(5-35 nm) silicon carbon nitride (SiCNH) dielectric as an oxidation and Cu diffusion barrier for damascene process is explored. The SiCNH cap's electrical properties, oxidation barrier performance, and the compositional depth profile analysis results showed that the scaling of the SiCNH cap is limited to 25 nm thickness. Without additional changes in current optimal SiCNH cap, 25 nm is the minimum required thickness for a reliable SiCNH cap in sub-30 nm Cu BEOL devices.
Hypertension in mesangial IgA glomerulonephritis. (1985)

Blood pressure in 75 patients with IgA nephropathy (IgA-GN), confirmed by renal biopsy, was related to clinical, immunological and morphological findings. The findings were compared with an age-matched control group of patients with non-IgA-GN. Overall prevalence of hypertension (HT) was similar in IgA-GN and non-IgA-GN (38.7% vs 38.2%). The presence of HT in IgA-GN was related to age, renal function, immunohistological pattern and degree of glomerular sclerosis or vascular lesions respectively. No correlation was found between HT and elevated serum IgA, circulating IgA immune complexes and IgA skin deposits. The current observations underline the value of hypertension for predicting development of renal failure. Vascular lesions are not only strongly correlated with, but may even precede development of, hypertension as confirmed by longitudinal observations.
Reliability Assessment of Breakwaters. (1997)

Abstract : In this report, several level II reliability techniques are discussed and applied to breakwater design. Using these methods, the reliability and reliability index are determined for the dominant performance functions of a breakwater including stone and concrete armor stability, concrete armor structural response, runup, and overflopping. The methods include Taylor series finite difference (TSFD) methods, which are shown to be easily computed using a handheld calculator or spreadsheet. The TSFD method is shown to yield reasonable accuracy for preliminary comparison of various alternatives. An invariant iterative TSFD method and associated FORTRAN program are shown, which provide an improved approximation to the reliability for design and evaluation purposes.
Consumption of cocoa flavanols results in acute improvements in mood and cognitive performance during sustained mental effort (2009)

Cocoa flavanols (CF) positively influence physiological processes in ways that suggest their consumption may improve aspects of cognitive function. This study investigated the acute cognitive and subjective effects of CF consumption during sustained mental demand. In this randomized, controlled, double-blinded, balanced, three period crossover trial 30 healthy adults consumed drinks containing 520 mg, 994 mg CF and a matched control, with a three-day washout between drinks. Assessments included the state anxiety inventory and repeated 10-min cycles of a Cognitive Demand Battery comprising of two serial subtraction tasks (Serial Threes and Serial Sevens), a Rapid Visual Information Processing (RVIP) task and a 'mental fatigue' scale, over the course of 1 h. Consumption of both 520 mg and 994 mg CF significantly improved Serial Threes performance. The 994 mg CF beverage significantly speeded RVIP responses but also resulted in more errors during Serial Sevens. Increases in self-reported 'mental fatigue' were significantly attenuated by the consumption of the 520 mg CF beverage only. This is the first report of acute cognitive improvements following CF consumption in healthy adults. While the mechanisms underlying the effects are unknown they may be related to known effects of CF on endothelial function and blood flow.
Integration of InP and InGaAs on 300 mm Si Wafers Using Chemical Mechanical Planarization (2016)

Integration of III-V high mobility channel materials in complementary metal oxide semiconductors (CMOS) and III-V photonic materials for integrated light sources on Si substrates requires low defect density III-V buffer layers in order to enable epitaxial growth of high crystal quality active layers. For the fabrication of In0.53Ga0.47As n-channel MOSFET on Si, a lattice matched InP buffer layer is one of the most effective approaches when used in combination with the aspect ratio trapping technique, an integration method known for reducing the density of defects formed during relaxation of strain induced by the lattice mismatch between InP and Si. The InP buffer should be planarized in order to improve thickness uniformity and roughness before subsequent deposition of active layers. In this work we discuss the development of InP planarization on 300 mm Si wafers and investigate slurry composition effects on the final oxide loss and condition of the InP surface. To further explore viability of this approach we deposited an epitaxial In0.53Ga0.47As n-MOS channel layer on top of the planarized InP buffer.
Amyloid Structure: Models and Theoretical Considerations in Fibrous Aggregates (2002)

Abstract In celebration of the many contributions to peptide chemistry from K.‐T. Wang's laboratory, this manuscript explores the structure of the Aβ(10–35) fibril. This central segment of the Aβ peptide of Alzheimer's Disease self‐assembles into well‐ordered paracrystalline arrays that seem to contradict many of the accepted paradigms established for soluble, globular proteins. Here we exploit initial molecular modeling efforts to assist in understanding these apparent contradictions. The emerging structure is one of a large self‐assembly of β‐strands, whose stability is dependent on large spatial and temporal fluctuation about a central core, giving rise to what can be best described as a dynamic and fluid tube‐like micelle. This fibril structure maintains features that are distinctly different from those of either synthetic or biological fibrils, and these differences have profound implications for biomedical intervention in amyloid diseases as well as for the design of self‐assembling nanoscale fibrils.
A Novel Model of Mixed Vascular Dementia Incorporating Hypertension in a Rat Model of Alzheimer’s Disease (2019)

Alzheimer's disease (AD) and mixed dementia (MxD) comprise the majority of dementia cases in the growing global aging population. MxD describes the coexistence of AD pathology with vascular pathology, including cerebral small vessel disease (SVD). Cardiovascular disease increases risk for AD and MxD, but mechanistic synergisms between the coexisting pathologies affecting dementia risk, progression and the ultimate clinical manifestations remain elusive. To explore the additive or synergistic interactions between AD and chronic hypertension, we developed a rat model of MxD, produced by breeding APPswe/PS1ΔE9 transgenes into the stroke-prone spontaneously hypertensive rat (SHRSP) background, resulting in the SHRSP/FAD model and three control groups (FAD, SHRSP and non-hypertensive WKY rats, <i>n</i> = 8-11, both sexes, 16-18 months of age). After behavioral testing, rats were euthanized, and tissue assessed for vascular, neuroinflammatory and AD pathology. Hypertension was preserved in the SHRSP/FAD cross. Results showed that SHRSP increased FAD-dependent neuroinflammation (microglia and astrocytes) and tau pathology, but plaque pathology changes were subtle, including fewer plaques with compact cores and slightly reduced plaque burden. Evidence for vascular pathology included a change in the distribution of astrocytic end-foot protein aquaporin-4, normally distributed in microvessels, but in SHRSP/FAD rats largely dissociated from vessels, appearing disorganized or redistributed into neuropil. Other evidence of SVD-like pathology included increased collagen IV staining in cerebral vessels and PECAM1 levels. We identified a plasma biomarker in SHRSP/FAD rats that was the only group to show increased Aqp-4 in plasma exosomes. Evidence of neuron damage in SHRSP/FAD rats included increased caspase-cleaved actin, loss of myelin and reduced calbindin staining in neurons. Further, there were mitochondrial deficits specific to SHRSP/FAD, notably the loss of complex II, accompanying FAD-dependent loss of mitochondrial complex I. Cognitive deficits exhibited by FAD rats were not exacerbated by the introduction of the SHRSP phenotype, nor was the hyperactivity phenotype associated with SHRSP altered by the FAD transgene. This novel rat model of MxD, encompassing an amyloidogenic transgene with a hypertensive phenotype, exhibits several features associated with human vascular or "mixed" dementia and may be a useful tool in delineating the pathophysiology of MxD and development of therapeutics.
Picosecond photoresponse in Y-Ba-Cu-O ultrathin films (1993)

We have applied a double-bridge voltage-correlation technique to study the nonequilibrium superconducting properties in high-${\mathit{T}}_{\mathit{c}}$ superconductors. Using Y-Ba-Cu-O thin films of thickness less than 15 nm, we have observed voltage pulses as fast as 40 ps. The temporal photoresponse signal was found to depend strongly on the sample's thickness. A systematic trend in the superconductivity decay time as a function of film thickness was obtained. The phonon-trapping effect has been verified to be the major limiting mechanism in the quasiparticle (QP) relaxation process. The role of electron-phonon coupling in the QP decay process has also been studied with 500-fs and 40-ps laser pulses.
Visible-light initiated oxidative cyclization of phenyl propiolates with sulfinic acids to coumarin derivatives under metal-free conditions (2015)

A visible-light initiated oxidative cyclization of phenyl propiolates with sulfinic acids has been developed. The arylsulfonylation of alkynes was performed at room temperature under metal-free conditions to generate coumarin derivatives with wide functional group tolerance, good yields and high regioselectivity.
Figure S2 from Phase I–II Open-Label Multicenter Study of Palbociclib + Vemurafenib in <i>BRAF</i><sup>V600MUT</sup> Metastatic Melanoma Patients: Uncovering CHEK2 as a Major Response Mechanism (2023)

&lt;p&gt;Figure S2. (A) Change in the tumor burden from baseline over time according to RECIST for all the included patients. The tumor burden was measured as the sum of the longest diameters of target lesions. Each line represents a patient. (B) Kaplan-Meier plot of the overall survival for all the included patients (N =18). (C) Kaplan-Meier plot of the progression-free survival for all the included patients (N =18).&lt;/p&gt;
Tempered Sigmoid Activations for Deep Learning with Differential Privacy (2020)

Because learning sometimes involves sensitive data, machine learning algorithms have been extended to offer privacy for training data. In practice, this has been mostly an afterthought, with privacy-preserving models obtained by re-running training with a different optimizer, but using the model architectures that already performed well in a non-privacy-preserving setting. This approach leads to less than ideal privacy/utility tradeoffs, as we show here. Instead, we propose that model architectures are chosen ab initio explicitly for privacy-preserving training. To provide guarantees under the gold standard of differential privacy, one must bound as strictly as possible how individual training points can possibly affect model updates. In this paper, we are the first to observe that the choice of activation function is central to bounding the sensitivity of privacy-preserving deep learning. We demonstrate analytically and experimentally how a general family of bounded activation functions, the tempered sigmoids, consistently outperform unbounded activation functions like ReLU. Using this paradigm, we achieve new state-of-the-art accuracy on MNIST, FashionMNIST, and CIFAR10 without any modification of the learning procedure fundamentals or differential privacy analysis.
Evaluation with evoked and spontaneous electromyography during lumbar instrumentation: a prospective study (1997)

The neuroanatomical structures that approximate the bony pedicles of the lumbar spine allow little room for technical error or compromise of the bone during pedicle screw insertion. Currently available neurophysiological monitoring techniques detect compromised bone and nerve root injury after it occurs. The purpose of this prospective study is to evaluate the reliability and efficacy of a unique neurophysiological monitoring technique. This technique provides immediate evaluation of pedicle cortical bone integrity in patients undergoing lumbar fusion with instrumentation by using electrified surgical instruments throughout the pedicle screw fusion procedure. Spontaneous electromyographic (EMG) activity was also monitored. Intraoperative evoked EMG stimulation was performed using a pedicle probe and feeler as monopolar stimulators during the insertion of 164 pedicle bone screws in 32 patients. The EMG response to subthreshold stimulation intensities indicated cortical bone compromise. Immediate and conclusive feedback via evoked EMG activity using stimulating pedicle probes in appropriate muscle groups was successful in identifying pedicle cortical bone compromise in four patients. One false-negative evoked EMG study was noted but was identified via spontaneous EMG activity. Intraoperative EMG monitoring alerted the surgeon that redirection of the pedicle probe or screw was necessary to avoid nerve root irritation or injury and served as an early warning system. Evoked EMG stimulation proved to be reliable and efficacious, especially when used in combination with spontaneous EMG. This technique may provide an added safeguard during implant placement procedures at centers where intraoperative neurophysiological monitoring is routinely performed.
A direct approach to identify closed loop Wiener systems, whose linear dynamics are open-loop unstable (2004)

A Wiener system is a series connection of a linear dynamic system followed by a static non-linearity. The identification of Wiener systems has been an active research topic for years. We extend the algorithm proposed by Zhao & Westwick, [Proceedings, ACC2003] (2003) to identify Wiener systems that are unstable in open loop, but being operated stably in a closed-loop configuration. The variant of the MOESP (multivariable output-error state space) algorithm developed in Y. Zhao & D.T. Westwick (2003) is used to identify a state space model of the linear part of a Wiener system operating in closed loop. Since the linear dynamics of the Wiener system are unstable in open loop, the output of the linear subsystem cannot be obtained by direct simulation. Without an estimate of the linear output, the nonlinearity can't be estimated. The main contribution of this paper is the design of an extended Kalman filter, which is used to estimate the states of the linear subsystem as well as the parameters of the nonlinearity.