gebhart/patrepeval huggingface dataset:
Hepatocyte growth factor induces hepatocyte proliferation in vivo and allows for efficient retroviral-mediated gene transfer in mice (1998)

Recombinant retroviral vectors are an attractive means of transferring genes into the liver because they integrate into the host cell genome and result in permanent gene expression. However, efficient in vivo gene transfer is limited by the requirement of active cell division for integration. Traditional approaches to induce liver proliferation have the disadvantage of inducing hepatocellular injury by delivery of toxins or by surgical partial hepatectomy. As a nontraumatic alternative, we show that exogenous hepatocyte growth factor (HGF) is a powerful and safe mitogen for the mature intact murine liver when delivered continuously into the portal vein. A 5-day infusion of human HGF (5 mg/kg/d) resulted in > 140% increase in relative liver mass, which returned to normal in 4 to 5 weeks. This clearly shows that an exogenous growth factor can induce robust liver proliferation in vivo. In addition, we show that the HGF-induced proliferation was independent of interleukin-6, an essential cytokine involved in liver regeneration after partial hepatectomy. When recombinant retroviral vectors were infused in combination with HGF, 30% of hepatocytes were stably transduced with no indication of hepatic injury or histopathology. These results show the ability to obtain a clinically relevant transduction efficiency with retroviral vectors in vivo without the prior induction of liver injury. The level of hepatic gene transfer achieved has the potential to be curative for a large number of genetic liver diseases.
The clinical potential of proteasome inhibition (2004)

The development of the proteasome inhibitor bortezomib is a prime example of successful bench-to-bedside research. NF-κB is implicated in the pathogenesis of multiple myeloma (MM), and bortezomib blocks NF-κB activation and its sequelae. Additional bortezomib mechanisms include interactions at the MM cell surface and mitochondrial level and in downstream apoptotic signaling. In the pivotal bortezomib study, the response rate was 35%; time to progression (TTP), 7 months; and median duration of response, 14.3 months. Responses were associated with improvements in quality of life, increases in laboratory parameters, and decreased transfusions. Bortezomib is thus indicated in the US for patients with relapsed, progressive MM and recommended for approval in Europe. The confirmatory phase III trial has been stopped early due to a significant improvement in TTP with bortezomib. The success of bortezomib in MM demonstrates the utility of targeting the tumour:host interaction and BM milieu, in addition to the tumour itself.
High‐conversion polymerization. VII. A definition of the explosive region and the influence of free volume on it (1980)

Abstract The easily observed autoacceleration of free radical Polymerization is defined as the explosive region and an arbitrary but quantitative definition of it is made. Using this definition it is shown that the explosive regions of solution polymerizations of methyl methacrylate occur at constant values of the product of polymer concentration times (molecular weight) 1/2 . This upholds the concept that polymer entanglements control the termination reaction in this region. It is also shown that this region does not, as previously suggested, occur at a constant value of free volume, but that free volume does play a role in determining the rate of termination at a given level of chain entanglements.
Comparative study of three ways of using Jatropha curcas vegetable oil in a direct injection diesel engine (2020)

Although vegetable oils are apparently an advantageous alternative fuel for direct use in traditional diesel engines with no modification necessary, in practice many problems are regularly discussed in the literature including filter clogging, breakage of certain types of injection pumps, and deposits of carbon on the cold parts of engines. Several technological solutions have been proposed to overcome these problems but the majority of papers discuss them individually and have not actually compared them in similar conditions. The purpose of the present study was to use the same experimental device to compare the three most widely recognised technological options for the use of Jatropha curcas vegetable oil as a fuel in a direct injection diesel engine: preheating, blending with diesel, and recirculating exhaust gases. Power output, specific consumption, thermal efficiency and exhaust gas emissions were compared to those of diesel used as the reference. The results obtained were similar for preheated and non-preheated Jatropha oil, but differed from the results obtained with diesel. Similar combustion performance and similar emissions were obtained with a blend of 20% Jatropha oil and diesel to those obtained with diesel alone. Exhaust gas recirculation (EGR) with Jatropha oil could lead to fouling in the combustion chamber. In contrast to widely accepted theory, this study also clearly demonstrates that the viscosity of vegetable oil is not the main cause of poorer combustion quality and, consequently, of deposits in the combustion chamber.
Goal-Oriented Strategic Modelling for Cancer Care in Systems of Systems Context Using the i* Framework (2018)

Cancer Care is considered as a System of Systems (SoS) which results from the collaboration of a set of independent socio and technical constituent systems, largely driven by stakeholders’ needs and goals at multiple levels in a cancer care organisation taking into consideration SoS high-level goals and the constituent systems-level individual goals. It’s challenging to manage these goals specially in such complex large-scale SoS arrangement. However, Goal-Oriented Requirements Engineering (GORE) is considered a promising approach in SoS context to adopt in order to identify, model and manage goals achieved by the overall SoS and its constituent systems. This paper is aimed at investigating the implications of using GORE approaches, and in particular the i* framework to model Cancer Care goals in SoS context. We propose a new process to extract i* elements and concepts from existing user documentation, a "Goals Referential Integrity (GRI)" model that is aimed at maintaining the integrity and consistency of both the SoS-level goals and the constituent systems-level goals, and a proposed i* Cancer Care Goal-Oriented model in Systems of Systems context applied to the Admission, Discharge, and Transfer (ADT) cross-sectional organisational processes of King Hussein Cancer Centre in Jordan.
Fast Summation at Nonequispaced Knots by NFFT (2003)

We develop a new algorithm for the fast computation of discrete sums $f(y_j) := \sum_{k=1}^N \alpha_k K(y_j-x_k)$ (j =1, . . ., M) based on the recently developed fast Fourier transform (FFT) at nonequispaced knots. Our algorithm, in particular our regularization procedure, is simply structured and can be easily adapted to different kernels K. Our method utilizes the widely known FFT and can consequently incorporate advanced FFT implementations. In summary, it requires ${\cal O} (N \log N +M)$ arithmetic operations. We prove error estimates to obtain clues about the choice of the involved parameters and present numerical examples in one and two dimensions.
ChemInform Abstract: Solid‐Phase Synthesis: Applications to Combinatorial Libraries (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure 4 from EMT-Derived Alterations in Glutamine Metabolism Sensitize Mesenchymal Breast Cells to mTOR Inhibition (2023)

&lt;p&gt;UPLC-MS label enrichment in various metabolites after culturing of D492 and D492M with A) 1-13C-glutamine and B) 5-13C-glutamine for 6 hours. Results are shown as mean + standard deviation (n = 3).&lt;/p&gt;
3D Modeling of Single-Domain and Multi-Domain Vertical Alignment LCDs for Direct-View and Microdisplay Geometries (2012)

We successfully developed a 3D liquid crystal display (LCD) modeling program and applied the program to modeling the single-domain vertical alignment (VA) and intrinsic fringe field controlled multi-domain vertical alignment (IFF MVA) LCDs. Our study showed that proper and stable IFF MVA operation was obtained in the microdisplay geometry but not in the direct-view geometry, whereas regular VA operation was obtained in the direct-view geometry but not in the microdisplay geometry.
Faculty Opinions recommendation of Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags. (2019)

d Systematic comparison of SNAP versus
A threonine zipper that mediates protein–protein interactions: Structure and prediction (2018)

We present the structure of an engineered protein-protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stabilized by close-packing of the Thr residues, with only one intermonomer hydrogen bond (H-bond) between two of the Thr residues. This Thr-rich interface provides a unique opportunity to study the behavior of Thr in the context of many other Thr residues. In previous work, we have shown that the side chain (χ<sub>1</sub> ) dihedral angles of interface and core Thr residues can be predicted with high accuracy using a hard sphere plus stereochemical constraint (HS) model. Here, we demonstrate that in the Thr-rich local environment of the Thr zipper structure, we are able to predict the χ<sub>1</sub> dihedral angles of most of the Thr residues. Some, however, are not well predicted by the HS model. We therefore employed explicitly solvated molecular dynamics (MD) simulations to further investigate the side chain conformations of these residues. The MD simulations illustrate the role that transient H-bonding to water, in combination with steric constraints, plays in determining the behavior of these Thr side chains. Broader Audience Statement: Protein-protein interactions are critical to life and the search for ways to disrupt adverse protein-protein interactions involved in disease is an ongoing area of drug discovery. We must better understand protein-protein interfaces, both to be able to disrupt existing ones and to engineer new ones for a variety of biotechnological applications. We have discovered and characterized an artificial Thr-rich protein-protein interface. This novel interface demonstrates a heretofore unknown property of Thr-rich surfaces: mediating protein-protein interactions.
Resolving neural states from optical neural response readout (2021)

Abstract We examine two types of information loss function encountered in optical neural recording—the uncertainty of neural states encoding an external stimulus and the incompleteness of information that laser-excited fluorescence can read out from these neural states. We show that, even though these uncertainties are of distinctly different nature, they can be treated on an equal footing against the Fisher information metric, revealing the fundamental information limits inherent in optical neural recording.
Ohm’s law for ion conduction in lithium and beyond-lithium battery electrolytes (2019)

The viability of next generation lithium and beyond-lithium battery technologies hinges on the development of electrolytes with improved performance. Comparing electrolytes is not straightforward as multiple electrochemical parameters affect the performance of an electrolyte. Additional complications arise due to the formation of concentration gradients in response to dc potentials. We propose a modified version of Ohm's law to analyze current through binary electrolytes driven by a small dc potential. We show that the proportionality constant in Ohm's law is given by the product of the ionic conductivity, κ, and the ratio of currents in the presence (i<sub>ss</sub>) and absence (i<sub>Ω</sub>) of concentration gradients, ρ<sub>+</sub>. The importance of ρ<sub>+</sub> was recognized by Evans et al. [Polymer 28, 2324 (1987)]. The product κρ<sub>+</sub> is used to rank order a collection of electrolytes. Ideally, both κ and ρ<sub>+</sub> should be maximized, but we observe a trade-off between these two parameters, resulting in an upper bound. This trade-off is analogous to the famous Robeson upper bound for permeability and selectivity in gas separation membranes. Designing polymer electrolytes that overcome this trade-off is an ambitious but worthwhile goal.
Vulnerability of conditional NCAM-deficient mice to develop stress-induced behavioral alterations (2011)

Previous studies in rodents showed that chronic stress induces structural and functional alterations in several brain regions, including shrinkage of the hippocampus and the prefrontal cortex, which are accompanied by cognitive and emotional disturbances. Reduced expression of the neural cell adhesion molecule (NCAM) following chronic stress has been proposed to be crucially involved in neuronal retraction and behavioral alterations. Since NCAM gene polymorphisms and altered expression of alternatively spliced NCAM isoforms have been associated with bipolar depression and schizophrenia in humans, we hypothesized that reduced expression of NCAM renders individuals more vulnerable to the deleterious effects of stress on behavior. Here, we specifically questioned whether mice in which the NCAM gene is inactivated in the forebrain by cre-recombinase under the control of the calcium-calmodulin-dependent kinase II promoter (conditional NCAM-deficient mice), display increased vulnerability to stress. We assessed the evolving of depressive-like behaviors and spatial learning and memory impairments following a subchronic stress protocol (2 weeks) that does not result in behavioral dysfunction, nor in altered NCAM expression, in wild-type mice. Indeed, while no behavioral alterations were detected in wild-type littermates after subchronic stress, conditional NCAM-deficient mice showed increased immobility in the tail suspension test and deficits in reversal spatial learning in the water maze. These findings indicate that diminished NCAM expression might be a critical vulnerability factor for the development of behavioral alterations by stress and further support a functional involvement of NCAM in stress-induced cognitive and emotional disturbances.
Effect of hypothermia on brain cell membrane function and energy metabolism after transient global hypoxia-ischemia in the newborn piglet (2001)

This study was done to determine the effects of hypothermia on brain cell membrane function and energy metabolism after transient hypoxia-ischemia (HI) in the newborn piglet. Cerebral HI was induced by temporarily complete occlusion of bilateral common carotid arteries with surgical clips and simultaneous breathing with 8% oxygen for 30 min, followed by release of carotid occlusion and normoxic ventilation for 4 hr. Rectal temperature was maintained between 38.0 and 39.0 degrees C in normothermic groups, and between 34.0 and 35.0 degrees C in hypothermic groups for 4 hr after HI. During HI, heart rate, glucose and lactate level in the blood and cerebrospinal fluid increased, and base excess, pH and blood pressure decreased significantly in both normothermic and hypothermic groups. After HI, these abnormalities returned to normal in normothermic group, but lactic acidosis persisted in hypothermic group. Decreased cerebral Na+,K+- ATPase activity and increased lipid peroxidation products, indicative of HI- induced brain injury, were more profound in hypothermic group than in normothermic group. Brain ATP and phosphocreatine levels were not different between normothermic and hypothermic groups. In summary, hypothermia applied immediately after HI for 4 hr did not improve the recovery of brain cell membrane function and energy metabolism in the newborn piglet.
Robust multimodal face and fingerprint fusion in the presence of spoofing attacks (2015)

Anti-spoofing is attracting growing interest in biometrics, considering the variety of fake materials and new means to attack biometric recognition systems. New unseen materials continuously challenge state-of-the-art spoofing detectors, suggesting for additional systematic approaches to target anti-spoofing. By incorporating liveness scores into the biometric fusion process, recognition accuracy can be enhanced, but traditional sum-rule based fusion algorithms are known to be highly sensitive to single spoofed instances. This paper investigates 1-median filtering as a spoofing-resistant generalised alternative to the sum-rule targeting the problem of partial multibiometric spoofing where m out of n biometric sources to be combined are attacked. Augmenting previous work, this paper investigates the dynamic detection and rejection of livenessrecognition pair outliers for spoofed samples in true multi-modal configuration with its inherent challenge of normalisation. As a further contribution, bootstrap aggregating (bagging) classifiers for fingerprint spoof-detection algorithm is presented. Experiments on the latest face video databases (Idiap Replay- Attack Database and CASIA Face Anti-Spoofing Database), and fingerprint spoofing database (Fingerprint Liveness Detection Competition 2013) illustrate the efficiency of proposed techniques.
Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion (2018)

To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.
A 16-bit 16MS/s SAR ADC with on-chip calibration in 55nm CMOS (2017)

This paper presents a SAR ADC that is much smaller and faster than the recently reported precision (16-bit and beyond) SAR ADCs [1, 2, 3]. In addition, it features low input capacitance and an efficient on-chip foreground calibration algorithm to fix bit weight errors. Several other enabling techniques are also used, including signal independent reference switching using reservoir capacitors to improve speed and reduce area, LSB repeats and ADC residue measurement to improve efficiency. The prototype achieves 97.5dB SFDR while operating at 16MS/s and consumes 16.3mW. It was fabricated in 55nm CMOS and occupies 0.55mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Effects of Genotype, Environment, and Feeding Antibiotics on Serum Concentrations of IGF-I and α α 1 -Acid Glycoprotein (1999)

It has long been known that management practices such as genetic selection, all-in/all-out (AIAO), segregated early weaning (SEW), and feeding diets containing antimicrobials have the potential to increase the efficiency of lean pork production. However, the physiological reasons for this increase in efficiency have yet to be fully discovered. It is common knowledge that pigs subjected to pathogens and other stressors do not reach their genetic lean growth potential. Possible blood-borne markers for lean growth potential and immune system activation include insulin-like growth factor-I (IGF-I) and α1-acid glycoprotein (AGP).
Bend loss in buffered over-moded opticalfibre: LP 11 mode and ‘whispering gallery’mode interaction (1994)

Bend loss in over-moded fibre has been measured as a function of temperature. For the LP11 mode, an oscillatory loss dependence on temperature was observed, caused by coupling between the LP11 mode and a ‘whispering gallery’ mode. These interactions could have a significant effect on singlemode cutoff wavelength measurements.
Management in Intractable Obstetric Haemorrhage: An Audit Study on 61 Cases (2001)

Abstract Objective: To refine the indications of bilateral hypogastric artery ligation (BHAL) and angiographic selective embolisation (ASE) in intractable obstetric haemorrhage. Design: an audit study. Setting: Tertiary care university hospital. Population and methods: Retrospective analysis of 61 cases of obstetric intractable post partum haemorrhage (PPH) initially managed either by hysterectomy or a conservative approach in a tertiary referral centre between 1983 and 1998. Procedures were reviewed as a primary (P) or secondary (S) attempt to arrest the haemorrhagic process. Results: Ten hysterectomies (5 P, 5 S), 49 BHAL (48 P, 1 S) and 9 ASE (8 P, 1S) were successfully performed in arresting the haemorrhagic process. There were 7 maternal deaths, 5 following hysterectomy and 2 following a conservative approach. Atony of the uterus was the main cause of haemorrhage ( n =21) and genital tract laceration was associated with the worst prognosis. Time-elapse between delivery and surgery appears to be the main prognostic factor. Nine patients became pregnant 1 to 4 years later following a conservative approach. Conclusions: ASE seems to be indicated in haemodynamically stable patients with birth canal trauma or uterine atony and clotting anomalies. BHAL is indicated when haemorrhage occurs after a cesarean section or when the patient is haemodynamically unstable. BHAL should be taught to Junior doctors in an attempt to decrease the number of patients transferred in tertiary referral centers for intractable PPH. This might also decrease the number of hysterectomies in intractable PPH.
Comparison of anion removal capacities of Octolig® and Cuprilig (2011)

Mixtures of sodium salts of phosphate, arsenate, and fluoride were used in chromatography and batch experiments to compare the capacity of two immobilized ligands (IMLIGs) to remove these anions: Octolig and its copper (II)-based metallolig, Cuprilig. The focus of this study was twofold. First, to find out which material, Octolig or Cuprilig, would remove these anions most effectively; and secondly to determine the optimal capacity for removal of representative anions. Removal capacity was evaluated by two methods: by chromatography and by a batch method. The methods gave identical results, but the batch method was more convenient. Cuprilig had a lower capacity for removal of phosphate than Octolig. The capability of Octolig for removing anions was: phosphate > arsenate > fluoride >>> chloride >>>> bromide. Replication of phosphate removal was good for a given batch of Octolig. Of three different samples of Octolig, two seemed to be alike based on the phosphate- removal capacity; the third was different on the basis of a Student's t-test. This distinction indicates the batch procedure could serve as a quality control/assurance technique.