gebhart/patrepeval huggingface dataset:
A comparison of modified Larson and ‘anatomic’ posterolateral corner reconstructions in knees with combined PCL and posterolateral corner deficiency (2008)

Different methods to reconstruct damaged posterolateral structures are available, but there has been little work studying their relative performance in combined PCL plus posterolateral corner (PLC) deficiency. We hypothesized that an 'anatomic' reconstruction with three graft bundles crossing the joint line would restore knee laxity closer to normal than a modified two-bundle Larson reconstruction. In a controlled laboratory study, the kinematics of cadaveric knees were measured electromagnetically with posterior drawer, external rotation, or varus rotation loads applied, with the knee at sequential stages: intact, PCL-deficient; PCL plus PLC-deficient; modified Larson reconstruction; anatomic PLC reconstruction. The graft bundles were tensioned sequentially to restore specific degrees of freedom to intact values of laxity at specific angles of knee flexion. A significant difference was not found between the two reconstructions. Both reconstructions restored external rotation and varus laxity to normal. Both restored posterior drawer to that caused by isolated PCL deficiency, but did not restore posterior laxity to normal. It was concluded that, with appropriate graft tensioning, both PLC reconstructions could restore both external rotation and varus laxity to normal, but not posterior drawer. The three-stranded anatomical reconstruction did not perform better than the modified two-strand Larson technique. Both of these isolated PLC reconstructions in knees with combined PCL plus PLC deficiency restored the knees to the laxity condition of an isolated PCL-deficiency, they could not reduce posterior drawer to normal.
Functional association of CD7 with phosphatidylinositol 3-kinase: interaction via a YEDM motif (1996)

Human CD7 is a 40 kDa protein expressed on thymocytes, early T, B, NK and myeloid lineage cells in bone marrow, and on mature T and NK cells. Previous studies suggested human CD7 may be involved in T and NK cell activation and/or adhesion, and that CD7-mediated cell activation may be transduced via the lipid kinase phosphatidylinositol 3-kinase (Pi3-kinase), a heterodimeric cytosolic protein consisting of an 85 kDa adaptor subunit that is coupled to a 110 kDa catalytic subunit. It has recently been shown that a sequence motif present in the cytoplasmic tall of both human and mouse CD7 bound with high affinity to recombinant SH2 domains present in the p85 subunit of Pi3-kinase. In this work, we used co-precipitation with anti-CD7 mAb 3A1 and recombinant p85 SH2-GST fusion proteins and peptide competition analysis to demonstrate that the cytoplasmic tail of CD7 interacts with a functional Pi3-kinase via the pTyr-X-X-Met motif. Furthermore, we show that cross-linking of CD7 markedly increased the amount of Pi3-kinase activity associated with CD7. The interaction of CD7 with the Pi3-kinase signal transduction pathway provides a mechanism for the previously observed functional responses attributed to CD7-mediated T and NK cell activation.
The role of whey acidic protein four-disulfide-core proteins in respiratory health and disease (2016)

Members of the whey acidic protein (WAP) or WAP four-disulfide-core (WFDC) family of proteins are a relatively under-explored family of low molecular weight proteins. The two most prominent WFDC proteins, secretory leukocyte protease inhibitor (SLPI) and elafin (or the precursor, trappin-2), have been shown to possess multiple functions including anti-protease, anti-bacterial, anti-viral and anti-inflammatory properties. It is therefore of no surprise that both SLPI and elafin/trappin-2 have been developed as potential therapeutics. Given the abundance of SLPI and elafin/trappin-2 in the human lung, most work in the area of WFDC research has focused on the role of WFDC proteins in protecting the lung from proteolytic attack. In this review, we will outline the current evidence regarding the expanding role of WFDC protein function with a focus on WFDC activity in lung disease as well as emerging data regarding the function of some of the more recently described WFDC proteins.
Endothelial injury and dysfunction in ischemic acute renal failure (2002)

Ischemic acute renal failure is the most common cause of acute renal failure in hospitalized patients and has an average mortality rate of 50%. Although epithelial and vascular smooth muscle cell abnormalities have been clearly delineated in association with this condition, the extent of endothelial injury and dysfunction has been difficult to document, primarily for anatomic reasons. However, endothelial tight junction separation and endothelial cell detachment, blebbing, and necrosis have been observed after ischemia in other organs. In addition, adenosine triphosphate depletion studies in cultured endothelial cells have demonstrated that multiple actin-based alterations occur in a reversible and duration-dependent fashion. After an ischemic insult, total renal blood flow returns toward normal, but marked, regional alterations occur. Most affected is the outer medullary or corticomedullary junction region where blood flow remains approximately 10% of normal. In this area, the microvasculature becomes congested. Interstitial edema, red blood cell trapping, leukocyte adherence, and extravasation all contribute to this congestion. Increased expression of both P selectin and E selectin has been documented in renal endothelial cells after ischemic injury, and treatment with antibodies to either intercellular adhesion molecule-1, P selectins, or E selectins has been shown to minimize renal injury. During ischemia in vivo and adenosine triphosphate depletion in cell culture studies, F-actin destruction occurs, with polymerization leading to accumulation of intracellular actin aggregates. By using multiphoton microscopy, Voxx software, and the Tie-2 mouse with selective endothelial cell green fluorescent protein expression driven by the Tie-2 promoter, we have been able to identify macrovascular and microvascular endothelial cells in four dimensions (three dimensions plus time) intravitally. By using Texas red-labeled large molecular weight dextrans, we can document blood flow and vascular dysfunction. Intravital studies using multiphoton imaging techniques can now be conducted to identify and quantify endothelial cell injury and dysfunction in functioning organs.
All polarization-maintaining Er fiber-based optical frequency combs with nonlinear amplifying loop mirror (2016)

A fully stabilized all polarization-maintaining Er frequency comb with a nonlinear amplifying loop mirror with below 0.2 rad carrier-envelope-offset frequency phase noise is demonstrated. The integrated timing jitter is measured as 40 attosecond from 10 kHz to 10 MHz, which is the lowest value of any Er fiber frequency comb to date.
[Economic analysis of rituximab in combination with cyclophosphamide, vincristine and prednisolone in the treatment of patients with advanced follicular lymphoma in Portugal]. (2011)

This study demonstrates that the combination R-CVP in previously untreated indolent NHL patients improves life expectancy and is a cost-effective alternative to CVP in Portugal.
Supplementary data and scripts for "An Atlas of Human Metabolism" (2019)

This repository contains the models, data, and scripts associated with the publication "An Atlas of Human Metabolism". The content is divided into three main directories, each containing their own README file containing instructions. tINIT_GEMs - Contains the genome-scale metabolic models (GEMs) generated in the study using the tINIT algorithm, as well as many scripts and datasets necessary to reproduce model generation, analyses, and figures. ec_GEMs - Contains the enzyme-constrained models (ecGEMs) generated in the study using the GECKO framework, as well as many scripts and datasets necessary to reproduce model generation, analyses, and figures. GEM_PRO - Contains the GEM-PRO dataframe with the protein structure information associated with the Human1 model.
Highly alignment tolerant optical HD-SDI interconnect (2012)

A cost effective optical HD-SDI interconnect based on a collimated beam was developed enabling fully passive alignment. It was successfully used to deliver a full HD video data via a 100-m long optical fiber.
District Energy Systems: A Collaborative Exchange of Results on Planning, Operation and Modelling for Energy Efficiency (2018)

Workshop organized by INDIGO project as a collaborative activity among EU funded projects in the area of District Heating and Cooling. The objective of the workshop was twofold: (1) to create a cluster of European funded projects working in the area of District Energy Systems; and (2) to create a networking opportunity in which to share experiences on the results and difficulties of the researches, and to identify synergies.
Design of Thin-Film Lateral SOI PIN Photodiodes with up to Tens of GHz Bandwidth (2011)

Short-distance optical communications and emerging optical storage (OS) systems increasingly require fast (i.e with Gigahertz to tens of Gigahertz bandwidth) and integrated Si photodetectors (Csutak et al., 2002; Hobenbild et al., 2003; Zimmermann, 2000). Thin-film SOI integrated devices appear as the best candidate to cope with these high-speed requirements, notably for the 10Gb/s Ethernet standard (Afzalian & Flandre, 2005; 2006.a; Csutak et al., 2002). For such bandwidths design trades-off between speed and responsivity are very severe and require a careful optimization (Afzalian & Flandre, 2006.b). In this context, accurate analytical modeling is very important for insight, rapid technology assessment for the given application, and/or rapid system design. There is however a lack of these accurate models in the literature so that time consuming devices simulations are often the only solution. In (Afzalian & Flandre, 2005), we have proposed such an accurate analytical model for the responsivity of thin-film SOI photodiodes. In here, thorough analytical modeling of AC performances of thin-film lateral SOI PIN photodiodeswill be addressed. Speed performances depend on a trade-off between transit time of carriers and a RC constant related to the photodiode and readout circuit combined impedances. We will first focus on the transit time limitation of the thin-film SOI PIN diodes (section 2). Then, we will model the complex diode impedance using an equivalent lumped circuit (section 3). For a lateral SOI PIN photodiode indeed, the usual approximation of considering only the depletion capacitance, Cd, reveals insufficient. Our original model, fully validated by Atlas 2D numerical simulations and measurements, allows for predicting and optimizing SOI PIN detectors speed performances for the target applications in function of technological constraints, in particular their intrinsic length, Li, which is their main design parameter.
Protein SIC Secreted from Streptococcus pyogenes Forms Complexes with Extracellular Histones That Boost Cytokine Production (2018)

Innate immunity relies on an effective recognition of the pathogenic microorganism as well as on endogenous danger signals. While bacteria in concert with their secreted virulence factors can cause a number of inflammatory reactions, danger signals released at the site of infection may in addition determine the amplitude of such responses and influence the outcome of the disease. Here, we report that protein SIC, Streptococcal Inhibitor of Complement, an abundant secreted protein from <i>Streptococcus pyogenes</i>, binds to extracellular histones, a group of danger signals released during necrotizing tissue damage. This interaction leads to the formation of large aggregates <i>in vitro</i>. Extracellular histones and SIC are abundantly expressed and seen colocalized in biopsies from patients with necrotizing soft-tissue infections caused by <i>S. pyogenes</i>. In addition, binding of SIC to histones neutralized their antimicrobial activity. Likewise, the ability of histones to induce hemolysis was inhibited in the presence of SIC. However, when added to whole blood, SIC was not able to block the pro-inflammatory effect of histones. Instead SIC boosted the histone-triggered release of a broad range of cytokines and chemokines, including IL-6, TNF-α, IL-8, IL-1β, IL-1ra, G-CSF, and IFN-γ. These results demonstrate that the interaction between SIC and histones has multiple effects on the host response to <i>S. pyogenes</i> infection.
Denoising Noisy Neural Networks: A Bayesian Approach With Compensation (2023)

Deep neural networks (DNNs) with noisy weights, which we refer to as noisy neural networks (NoisyNNs), arise from the training and inference of DNNs in the presence of noise. NoisyNNs emerge in many new applications, including the wireless transmission of DNNs, the efficient deployment or storage of DNNs in analog devices, and the truncation or quantization of DNN weights. This paper studies a fundamental problem of NoisyNNs: how to reconstruct the DNN weights from their noisy manifestations. While prior works relied exclusively on the maximum likelihood (ML) estimation, this paper puts forth a denoising approach to reconstruct DNNs with the aim of maximizing the inference accuracy of the reconstructed models. The superiority of our denoiser is rigorously proven in two small-scale problems, wherein we consider a quadratic neural network function and a shallow feedforward neural network, respectively. When applied to advanced learning tasks with modern DNN architectures, our denoiser exhibits significantly better performance than the ML estimator. Consider the average test accuracy of the denoised DNN model versus the weight variance to noise power ratio (WNR) performance. When denoising a noisy ResNet34 model arising from noisy inference, our denoiser outperforms ML estimation by up to 4.1 dB to achieve a test accuracy of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$60\%$</tex-math></inline-formula> . When denoising a noisy ResNet18 model arising from noisy training, our denoiser outperforms ML estimation by 13.4 dB and 8.3 dB to achieve test accuracies of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$60\%$</tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$80\%$</tex-math></inline-formula> , respectively.
A new humanized antibody is effective against pathogenic fungi in vitro (2021)

Invasive fungal infections mainly affect patients undergoing transplantation, surgery, neoplastic disease, immunocompromised subjects and premature infants, and cause over 1.5 million deaths every year. The most common fungi isolated in invasive diseases are Candida spp., Cryptococcus spp., and Aspergillus spp. and even if four classes of antifungals are available (Azoles, Echinocandins, Polyenes and Pyrimidine analogues), the side effects of drugs and fungal acquired and innate resistance represent the major hurdles to be overcome. Monoclonal antibodies are powerful tools currently used as diagnostic and therapeutic agents in different clinical contexts but not yet developed for the treatment of invasive fungal infections. In this paper we report the development of the first humanized monoclonal antibody specific for β-1,3 glucans, a vital component of several pathogenic fungi. H5K1 has been tested on C. auris, one of the most urgent threats and resulted efficient both alone and in combination with Caspofungin and Amphotericin B showing an enhancement effect. Our results support further preclinical and clinical developments for the use of H5K1 in the treatment of patients in need.
The “Communovirus,” (In)Equality, and Justice (2020)

A Covid-19 poster’s warning to “Do Your Part/Stay Apart” and a dance sequence from Jean-Luc Godard’s 1964 film Bande à Part are the starting points for a reflection on Jean-Luc Nancy’s recent essay, “Communovirus,” in which he argues that the threat of the coronavirus “communizes us” even as it forces us to distance ourselves from each other. This paradoxical sense of shared separation, central to Nancy’s thought, is then explored in relation to the themes of (in)equality and justice in the context of the Covid-19 pandemic.
Compiler and runtime support for out-of-core HPF programs (1994)

This paper describes the design of a compiler which can translate out-of-core programs written in a data parallel language like HPF. Such a compiler is required for compiling large scale scientific applications, such as the Grand Challenge applications, which deal with enormous quantities of data. We propose a framework by which a compiler together with appropriate runtime support can translate an out-of-core HPF program to a message passing node program with explicit parallel I/O. We describe the basic model of the compiler and the various transformations made by the compiler. We also discuss the runtime routines used by the compiler for I/O and communication. In order to minimize I/O, the runtime support system can reuse data already fetched into memory. The working of the compiler is illustrated using two out-of-core applications, namely a Laplace equation solver and LU Decomposition, together with performance results on the Intel Touchstone Delta.
On subspace based sinusoidal frequency estimation (1999)

Subspace based methods for frequency estimation rely on a low-rank system model that is obtained by collecting the observed scalar valued data samples into vectors. Estimators such as MUSIC and ESPRIT have for some time been applied to this vector model. Also, a statistically attractive Markov-like procedure for this class of methods has been proposed in the literature. Herein, the Markov estimator is re-investigated. Several results regarding rank, performance, and structure are given in a compact manner. The results are used to establish the large sample equivalence of the Markov estimator and the approximate maximum likelihood (AML) algorithm proposed by Stoica et al. (see Automatica, vol.30, no.1, p.131-45, 1994).
Supplementary Figure S4 from The CARMA3–Bcl10–MALT1 Signalosome Drives NFκB Activation and Promotes Aggressiveness in Angiotensin II Receptor–Positive Breast Cancer (2023)

&lt;p&gt;Role of CARMA3 and MALT1 in mediating 2D proliferation and 3D spheroid growth.&lt;/p&gt;
Purification and properties of hamster liver ligandins, glutathione S-transferases. (1980)

Glutathione S-transferases have been purified to homogeneity from Chinese hamster liver. Three enzyme forms were separated and designated Forms I, II, and III in order of their elution from carboxymethylcellulose columns. The forms exhibit close physical similarities to glutathione S-transferases B (ligandin) of rat liver and epsilon of humam liver. However, enzyme kinetic analysis indicates that the hamster enzymes exhibit similar Km values but higher Vmax values towards common substrates compared with the rat and human forms. These differences, which explain the increased enzymic activities of hamster glutathione S-transferases in vivo and in vitro, appear to be related to slight differences in the peptide composition of hamster liver glutathione S-transferases compared to the rat and human enzymes.
ChemInform Abstract: f‐Element/Crown Ether Complexes. Part 16. Synthesis, Crystallization and Crystal Structure of (Dy(OH2)8)Cl3·18‐crown‐6·4 H2O. (1988)

Abstract The known complex (I) is thermally unstable and when it is allowed to warm up under the original solvent mixture, it redissolves and the title complex (II) is obtained.
Rectal Organoid Morphology Analysis (ROMA): A Diagnostic Assay in Cystic Fibrosis (2022)

Diagnosis of cystic fibrosis (CF) is not always straightforward, especially when sweat chloride concentration is intermediate and/or less than two disease-causing CFTR mutations can be identified. Physiological CFTR assays (nasal potential difference, intestinal current measurement) have been included in the diagnostic algorithm but are not always readily available or feasible (e.g., in infants). Rectal organoids are 3D structures that grow from stem cells isolated from crypts of a rectal biopsy when cultured under specific conditions. Organoids from non-CF subjects have a round shape and a fluid-filled lumen, as CFTR-mediated chloride transport drives water into the lumen. Organoids with defective CFTR function do not swell, retaining an irregular shape and having no visible lumen. Differences in morphology between CF and non-CF organoids are quantified in the 'Rectal Organoid Morphology Analysis' (ROMA) as a novel CFTR physiological assay. For the ROMA assay, organoids are plated in 96-well plates, stained with calcein, and imaged in a confocal microscope. Morphological differences are quantified using two indexes: The circularity index (CI) quantifies the roundness of organoids, and the intensity ratio (IR) is a measure of the presence of a central lumen. Non-CF organoids have a high CI and low IR compared to CF organoids. ROMA indexes perfectly discriminated 167 subjects with CF from 22 subjects without CF, making ROMA an appealing physiological CFTR assay to aid in CF diagnosis. Rectal biopsies can be routinely performed at all ages in most hospitals and tissue can be sent to a central lab for organoid culture and ROMA. In the future, ROMA might also be applied to test the efficacy of CFTR modulators in vitro. The aim of the present report is to fully explain the methods used for ROMA, to allow replication in other labs.
A dynamic logic circuit embedded flip-flop for ASIC design (2002)

We report a flip-flop with a dynamic logic circuit for data path designed with standard cell. The flip-flop provides fast logic operation by the dynamic logic circuit and reduces total power dissipation of a data path by suppressing glitches. An absolute difference unit for motion estimation is used in a benchmark test. By using the flip-flop, the unit is 20% to 40% faster and has 20% to 50% less power dissipation than when conventional D-FFs are used.
Figure S5 from UGT2B17 Expedites Progression of Castration-Resistant Prostate Cancers by Promoting Ligand-Independent AR Signaling (2023)

&lt;p&gt;Figure S5: UGT2B17 protein expression is correlated with pAR Y534 and pSrc Y416 levels in PCa cell lines&lt;/p&gt;
ChemInform Abstract: Synthesis of Homorhamnojirimycins (I) and Related Trihydroxypipecolic Acid Derivatives (II) and (III) via Divergent Bicyclic Amino Lactone Intermediates: Inhibition of Naringinase (L‐Rhamnosidase) and dTDP‐Rhamnose Biosynthesis. (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.
Far Region Boundary Definition of Linear Massive MIMO Antenna Arrays (2015)

The plane wave assumption has been used extensively in wireless channel modeling for simplicity. However, when the plane wave model is applied to the massive multiple input and multiple output (MIMO) channel characterization, it is no longer suitable. In this paper, by using the geometrical channel parameterizations, the phase shift difference caused by the spherical wave for a large linear antenna array is investigated, and the Far Region Boundary of a Linear Massive Antenna has been proposed as a criterion to determine whether the user terminal is within the near field of this large antenna structure. Finally, by using ray-tracing method, the proposed boundary within which the propagation caused phase difference exceeds 22.5 is verified. The spherical wave model is necessary for the more accurate channel characterization.