gebhart/patrepeval huggingface dataset:
Structural analysis of avibactam-mediated activation of the bla and mec divergons in methicillin-resistant Staphylococcus aureus (2020)

Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) infections cause significant mortality and morbidity globally. MRSA resistance to β-lactam antibiotics is mediated by two divergons that control levels of a β-lactamase, PC1, and a penicillin-binding protein poorly acylated by β-lactam antibiotics, PBP2a. Expression of genes encoding these proteins is controlled by two integral membrane proteins, BlaR1 and MecR1, which both have an extracellular β-lactam-binding sensor domain. Here, we solved the X-ray crystallographic structures of the BlaR1 and MecR1 sensor domains in complex with avibactam, a diazabicyclooctane β-lactamase inhibitor at 1.6-2.0 Å resolution. Additionally, we show that <i>S. aureus</i> SF8300, a clinically relevant strain from the USA300 clone of MRSA, responds to avibactam by up-regulating the expression of the <i>blaZ</i> and <i>pbp2a</i> antibiotic-resistance genes, encoding PC1 and PBP2a, respectively. The BlaR1-avibactam structure of the carbamoyl-enzyme intermediate revealed that avibactam is bound to the active-site serine in two orientations ∼180° to each other. Although a physiological role of the observed alternative pose remains to be validated, our structural results hint at the presence of a secondary sulfate-binding pocket that could be exploited in the design of future inhibitors of BlaR1/MecR1 sensor domains or the structurally similar class D β-lactamases. The MecR1-avibactam structure adopted a singular avibactam orientation similar to one of the two states observed in the BlaR1-avibactam structure. Given avibactam up-regulates expression of <i>blaZ</i> and <i>pbp2a</i> antibiotic resistance genes, we suggest further consideration and research is needed to explore what effects administering β-lactam-avibactam combinations have on treating MRSA infections.
Correction to: Extracellular Vesicles: Biomarkers, Therapeutics, and Vehicles in the Visual System (2018)

[This corrects the article DOI: 10.1007/s40135-017-0153-0.].
A Novel Relay-Aided Transmission Scheme in Cognitive Radio Networks (2011)

In underlay cognitive radio networks, unlicensed secondary users are allowed to share the spectrum with licensed primary users when the interference induced on the primary transmission is limited. In this paper, we propose a new cooperative transmission scheme for cognitive radio networks where a relay node is able to help both the primary and secondary transmissions. We derive exact closed-form and upper bound expressions of the conditional primary and secondary outage probabilities over Rayleigh fading channels. Furthermore, we proposed a simple power allocation algorithm. Finally, using numerical evaluation and simulation results we show the potential of our cooperative transmission scheme in improving the secondary outage probability without harming the primary one.
Immune dysregulation to Ethiopian immigrants in Israel: relevance to helminth infections? (1996)

SUMMARY The infectious disease background and particularly the helminth infections that are endemic in Africa could have profound effects on the host immune system. Studies that we have performed on an Ethiopian HIV− immigrant population that has recently reached Israel, lend support to this notion. They have indeed revealed a very high prevalence of helminth and several other infections with an extreme immune dysregulation, consisting of: (i) highly elevated plasma IgE, IgG, placental isoferritin, p75 soluble TNF receptor (sTNFR) levels and very high blood eosinophilia; (ii) increased secretion from phytohaemagglutinin (PHA)-simulated peripheral blood mononuclear cells (PBMC) of the cytokines IL-2, IL-4, IL-10 and p75s sTNFR, and decreased secretion of interferon-gamma (IFN-γ) and IL-6; (iii) increased and decreased surface expression of p75 TNFR and IL-6 receptor on lymphocytes, respectively. The causal relationship between this immune dysregulation and the infectious background is highly suggestive, and could have far-reaching implications in the resistance to other infections.
Ausdehnung der Lymphknotendissektion nach minimalinvasiver Ösophagusresektion? (2006)

Our experience with 25 successful minimally invasive esophageal resections shows that with increasing experience and better surgical equipment, the extent of lymph node dissection does not differ from open procedure.
Combination of inositol and alpha lipoic acid in metabolic syndrome-affected women: a randomized placebo-controlled trial (2013)

Current Controlled Trial ISRCTN74096908.
Theoretical models and operational procedures for feasibility studies of new cabotage lines (2003)

The present condition of freight transport system, unbalanced strongly toward the road transport, with remarkable costs both in terms of environment impact and of safety, pushes a relaunching of the combined road-sea transport and so of the maritime way. The paper proposes a methodological approach, founded on theoretical models, for feasibility studies of new cabotage lines, useful to orient the sector operators in the identifying efficient and effective sabotage services.&#13;\nAfter a short recall to the problems concerning the sabotage, some transport supply models are illustrated for sea and road transport as alternative modes. As concerns the transport demand, an estimation procedure based on RP/SP surveys, is suggested.&#13;\nThe proposed models are applied for a comparative analysis of the road, railway and maritime transport alternatives between two Italian regions, taking into consideration also two different charge units: lorry with tractor and lorry without tractor. The analysis is made both according to a MTO and a Maritime Operator.&#13;\nSome feasibility studies of new sabotage lines in the Mediterranean Sea are under widening. The research can turn out a valid tool to orient the sector operators and contribute to avoid failures such as some recent cases in the Mediterranean Europe.
Hydrogen Peroxide Signaling in Plant Development and Abiotic Responses: Crosstalk with Nitric Oxide and Calcium (2016)

Hydrogen peroxide (H2O2), as a reactive oxygen species, is widely generated in many biological systems. It has been considered as an important signaling molecule that mediates various physiological and biochemical processes in plants. Normal metabolism in plant cells results in H2O2 generation, from a variety of sources. Also, it is now clear that nitric oxide (NO) and calcium (Ca(2+)) function as signaling molecules in plants. Both H2O2 and NO are involved in plant development and abiotic responses. A wide range of evidences suggest that NO could be generated under similar stress conditions and with similar kinetics as H2O2. The interplay between H2O2 and NO has important functional implications to modulate transduction processes in plants. Moreover, close interaction also exists between H2O2 and Ca(2+) in response to development and abiotic stresses in plants. Cellular responses to H2O2 and Ca(2+) signaling systems are complex. There is quite a bit of interaction between H2O2 and Ca(2+) signaling in responses to several stimuli. This review aims to introduce these evidences in our understanding of the crosstalk among H2O2, NO, and Ca(2+) signaling which regulates plant growth and development, and other cellular and physiological responses to abiotic stresses.
3D kidney segmentation from abdominal diffusion MRI using an appearance-guided deformable boundary (2018)

A new technique for more accurate automatic segmentation of the kidney from its surrounding abdominal structures in diffusion-weighted magnetic resonance imaging (DW-MRI) is presented. This approach combines a new 3D probabilistic shape model of the kidney with a first-order appearance model and fourth-order spatial model of the diffusion-weighted signal intensity to guide the evolution of a 3D geometric deformable model. The probabilistic shape model was built from labeled training datasets to produce a spatially variant, independent random field of region labels. A Markov-Gibbs random field spatial model with up to fourth-order interactions was adequate to capture the inhomogeneity of renal tissues in the DW-MRI signal. A new analytical approach estimated the Gibbs potentials directly from the DW-MRI data to be segmented, in order that the segmentation procedure would be fully automatic. Finally, to better distinguish the kidney object from the surrounding tissues, marginal gray level distributions inside and outside of the deformable boundary were modeled with adaptive linear combinations of discrete Gaussians (first-order appearance model). The approach was tested on a cohort of 64 DW-MRI datasets with b-values ranging from 50 to 1000 s/mm2. The performance of the presented approach was evaluated using leave-one-subject-out cross validation and compared against three other well-known segmentation methods applied to the same DW-MRI data using the following evaluation metrics: 1) the Dice similarity coefficient (DSC); 2) the 95-percentile modified Hausdorff distance (MHD); and 3) the percentage kidney volume difference (PKVD). High performance of the new approach was confirmed by the high DSC (0.95±0.01), low MHD (3.9±0.76) mm, and low PKVD (9.5±2.2)% relative to manual segmentation by an MR expert (a board certified radiologist).
Comparison of Gene Expression Profiles between Keratinocytes, Melanocytes and Fibroblasts (2013)

Our data provide important information on which to base further investigation into the specification of skin cell types.
Intelligent docking for an autonomous ocean sampling network (2002)

Examines the complexities associated with docking for autonomous underwater vehicles (AUVs) operating within an autonomous ocean sampling network. By looking at the different stages in a typical mission profile for a number of actual runs, the authors can qualitatively estimate failure rates for each of the different stages of docking. The authors examine statistics for the following stages - undocking and launching the vehicle; completing the mission; returning to the vicinity of the dock; turning on the homing beacon; homing into the dock; latching onto the dock; and finally aligning inductive cores for power transfer. Despite differing probabilities of success for the individual stages, the authors show that the redundancy associated with retrying each stage until the exit condition is met, is sufficient to yield a very high overall system reliability.
Identifying and Rectifying Rational Gaps in Fuzzy Rule Based Systems for Regression Problems (2021)

Fuzzy Rule Based Systems (FRBSs) can suffer from incomplete and sparse rule bases as a result of selecting a small number of rules from a large universe of potential rules. This may lead to rational gaps creeping into the input output mapping, where sometimes, strongly correlated inputs displaying a linear relationship with the output do not exhibit the same behaviour during inferencing. This paper proposes a technique for identifying and rectifying such gaps for FRBSs using incomplete rule bases in real-world regression problems.
Mechanical Load Increases in Bone Formation via a Sclerostin-Independent Pathway (2014)

Sclerostin, encoded by the Sost gene, is an important negative regulator of bone formation that has been proposed to have a key role in regulating the response to mechanical loading. To investigate the effect of long-term Sclerostin deficiency on mechanotransduction in bone, we performed experiments on unloaded or loaded tibiae of 10 week old female Sost-/- and wild type mice. Unloading was induced via 0.5U botulinum toxin (BTX) injections into the right quadriceps and calf muscles, causing muscle paralysis and limb disuse. On a separate group of mice, increased loading was performed on the left tibiae through unilateral cyclic axial compression of equivalent strains (+1200 µe) at 1200 cycles/day, 5 days/week. Another cohort of mice receiving equivalent loads (-9.0 N) also were assessed. Contralateral tibiae served as normal load controls. Loaded/unloaded and normal load tibiae were assessed at day 14 for bone volume (BV) and formation changes. Loss of BV was seen in the unloaded tibiae of wild type mice, but BV was not different between normal load and unloaded Sost-/- tibiae. An increase in BV was seen in the loaded tibiae of wild type and Sost-/- mice over their normal load controls. The increased BV was associated with significantly increased mid-shaft periosteal mineralizing surface/bone surface (MS/BS), mineral apposition rate (MAR), and bone formation rate/bone surface (BFR/BS), and endosteal MAR and BFR/BS. Notably, loading induced a greater increase in periosteal MAR and BFR/BS in Sost-/- mice than in wild type controls. Thus, long-term Sclerostin deficiency inhibits the bone loss normally induced with decreased mechanical load, but it can augment the increase in bone formation with increased load.
CCR5Δ32 and promoter polymorphisms are not correlated with initial virological or immunological treatment response (2001)

CCR5Delta32 and promoter genotypes may not be of clinical relevance in predicting initial virological or immunological response to antiretroviral therapy.
Production of micron-sized monodispersed polymer particles by seeded polymerization for the dispersion of highly monomer-swollen particles prepared with submicron-sized polymer seed particles utilizing the dynamic swelling method (1998)

For the purpose of extending the size range of polymer seed particles used in “dynamic swelling method” (DSM), first it was verified theoretically that the submicron-sized polymer particles produced by emulsion polymerization can also absorb a large amount of monomer by DSM in both equilibrium and kinetic control states. Next, on the basis of the theoretical results, experimentally about 2.6 μm-sized styrene-swollen polystyrene (PS) particles were prepared utilizing DSM in the presence of 0.64 μm-sized monodispersed PS seed particles produced by emulsifier-free emulsion polymerization. Moreover, 2.5 μm-sized monodispersed PS particles were produced by the addition of cupric chloride as a water-soluble inhibitor to depress the by-production of submicron-sized PS particles in the seeded polymerization at 30°C with 2,2′-azobis(4-methoxy-2,4-dimethylvaleronitrile) initiator. © 1998 John Wiley & Sons, Inc. J. Polym. Sci. A Polym. Chem. 36: 2513–2519, 1998
RARE: Image Reconstruction Using Deep Priors Learned Without Groundtruth (2020)

Regularization by denoising (RED) is an image reconstruction framework that uses an image denoiser as a prior. Recent work has shown the state-of-the-art performance of RED with learned denoisers corresponding to pre-trained convolutional neural nets (CNNs). In this work, we propose to broaden the current denoiser-centric view of RED by considering priors corresponding to networks trained for more general artifact-removal. The key benefit of the proposed family of algorithms, called regularization by artifact-removal (RARE), is that it can leverage priors learned on datasets containing only undersampled measurements. This makes RARE applicable to problems where it is practically impossible to have fully-sampled groundtruth data for training. We validate RARE on both simulated and experimentally collected data by reconstructing a free-breathing whole-body 3D MRIs into ten respiratory phases from heavily undersampled k-space measurements. Our results corroborate the potential of learning regularizers for iterative inversion directly on undersampled and noisy measurements.
Nitrogen pair luminescence in GaAs (1990)

We report on the first observation of different nitrogen pair complexes in GaAs. These complexes, which have been searched for since the ’60s, are studied under the application of hydrostatic pressure. By carefully tuning the pressure, we make one after the other of the NNi pairs (1≤i≤10) appear in the band gap of GaAs and then become the major exciton recombination channel. We compare our results for nitrogen states in GaAs with the classical case of NNi excitons in GaP.
Retrofitting of AYALA Bridge, an historic steel bridge in Manilla (Philippines) (2016)

&lt;p&gt;Ayala Bridge, in the center of Manilla, is a steel arch bridge built in the 1950s. It is comprised of 2 simply supported steel bridges constructed with 3 trusses connected together. The bridge has to be retrofitted for conformity to new codes (traffic and seismic) and lifted by 70 cm for conformity to regulatory clearance. The retrofitting solution designed by Freyssinet was chosen because of its economy when considering both deck and foundations: it consists of minimizing the current seismic loads on piers and abutments, to get them lower than actual loads seen in the past under historic seismic and typhoon. Longitudinally, the 2 decks are linked together and extended with beams and new piles: the overall structure is working as a frame. Transversally, some seismic devices are placed. The overall steel structure is then strengthened using additional steel profiling and prestressing. Major parts of the work has been done with no traffic interruption at all.&lt;/p&gt;
ChemInform Abstract: Enantioselective Oxidation of 2‐Methyl‐1‐alkanols by Alcohol Oxidase from Methylotrophic Yeasts. (1995)

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.
P2‐189: CHRONOLOGICAL CORRELATION BETWEEN LSD1, β‐AMYLOID AND PRO‐INFLAMMATORY MARKERS WITH COGNITIVE PERFORMANCE IN AN AD‐LIKE TRANSGENIC RAT MODEL (2018)

Lysine-specific demethylase 1 (LSD1) function as a transcriptional repressor or activator by demethylation of histone H3 on lysine 4 or 9 and regulates different physiological processes including inflammatory responses and learning and memory. In the present study, we investigate chronological hippocampal levels of LSD1 and its correlation with the expression of pro-inflammatory markers, analyzing simultaneously β-amyloid levels and cognitive performance of our transgenic AD-like rats. We used the hemizygous McGill-R-Thy1-APP transgenic rats, which progressively accumulates intraneuronal Aβ peptide and display cognitive deficits (Leon, et al. 2010). Posterior to cognitive status test assessed by Morris water maze, hippocampal β-amyloid accumulation, LSD1 levels and inflammatory protein markers expression were measured by western blot at different ages (3, 6, 12 and 18 months old) of non-transgenic (APP-/-) and hemizygous (APP+/-) transgenic rats. Increased levels of LSD1 at very early stages of the amyloid pathology (6 months old) in hippocampus of APP+/- transgenic rats displayed a positive correlation through age during the progression of Aβ pathology (Pearson r2=0.77 (6 months); 0.87 (12 months) and 0.82 (18 months), respectively p<0.05). Furthermore, we observe a strong positive correlation between LSD1 and the expression of certain inflammatory markers such as IL1- β, nNOS and Cox-2. Surprisingly, we found a negative correlation between hippocampal TNF-α levels and LSD-1 suggesting that increased protein expression of LSD1 may interfere negatively in TNF-α gene expression. Behavioral studies showed deficits in cognitive performance beginning at 18 months old of hemizygous transgenic rats compared to non-transgenic aged matched rats. In our model, hippocampal LSD1 levels begins to increase at very early stages of amyloid pathology, suggesting a possible epigenetic protective mechanism by which, transgenic rats, could trigger to preserve cognitive functions in response to the progressive β-amyloid accumulation. However, starting at 18 months of age, the excessive accumulation of Aβ display a positive correlation with cognitive deficits and also with LSD1 levels, not perceived at previous ages and not observed in non-transgenic age-matched controls. We reasoned that increased LSD1 expression would contribute to pro-inflammatory markers deregulation pointing LSD1 as a candidate target for further clinical manipulation.
Intra-WZ quantization mismatch in distributed video coding (2011)

During the past decade, Distributed Video Coding (DVC) has emerged as a new video coding paradigm, shifting the complexity from the encoder - to the decoder-side. This paper addresses a problem of current DVC architectures that has not been studied in the literature so far, that is, the mismatch between the intra and Wyner-Ziv (WZ) quantization processes. Due to this mismatch, WZ rate is spent even for spatial regions that are accurately approximated by the side-information. As a solution, this paper proposes side-information generation using selective unidirectional motion compensation from temporally adjacent WZ frames. Experimental results show that the proposed approach yields promising WZ rate gains of up to 7% relative to the conventional method.
Subvastus (Southern) Approach for Primary Total Knee Arthroplasty (1991)

The subvastus or Southern approach to the knee had been described as early as 1929 but is not found in standard modern orthopedic textbooks. This approach for primary total knee arthroplasty (TKA) preserves the integrity of the extensor mechanism and maintains the vascular supply to the patella. To appreciate the potential benefits of this approach, a complete understanding of the surgical anatomy is essential. The benefits of the subvastus approach make it a valuable technique for primary TKA.
ChemInform Abstract: Solution to the C3—Arylation of Indazoles: Development of a Scalable Method. (2016)

Abstract The title transformation is achieved following a Negishi coupling protocol which tolerates variously functionalized aryl and hetaryl bromides.
The therapeutic monoclonal antibody market (2014)

Since the commercialization of the first therapeutic monoclonal antibody product in 1986, this class of biopharmaceutical products has grown significantly so that, as of November 10, 2014, forty-seven monoclonal antibody products have been approved in the US or Europe for the treatment of a variety of diseases, and many of these products have also been approved for other global markets. At the current approval rate of ∼ four new products per year, ∼70 monoclonal antibody products will be on the market by 2020, and combined world-wide sales will be nearly $125 billion.
Vico and Moral Perception (1997)

Vico and Moral Perception maintains that Vico's New Science offers an idiosyncratic theory of ethics that rejects the modernist notion of "principle" but which at the same time promotes an "historical absolutism" that post-modern thought denies. Vico's account of civic metaphor not only responds effectively to questions of moral agency but provides a unique cultural and rhetorical framework for studying the contexts of attention, the entry points of conscience, that anchor moral perception