gebhart/patrepeval huggingface dataset:
Rolled‐out Wordles: A Heuristic Method for Overlap Removal of 2D Data Representatives (2012)

Abstract When representing 2D data points with spacious objects such as labels, overlap can occur. We present a simple algorithm which modifies the (Mani‐) Wordle idea with scan‐line based techniques to allow a better placement. We give an introduction to common placement techniques from different fields and compare our method to these techniques w.r.t. euclidean displacement, changes in orthogonal ordering as well as shape and size preservation. Especially in dense scenarios our method preserves the overall shape better than known techniques and allows a good trade‐off between the other measures. Applications on real world data are given and discussed.
Introduction of a free cysteinyl residue at position 68 in the subtilisin Savinase, based on homology with proteinase K (1992)

Two subfamilies of the subtilisins, distinguished by the presence or absence of a free cysteinyl residue near the essential histidyl residue of the catalytic triad, are known. In order to evaluate the significance of the presence of this -SH group a cysteinyl residue has been introduced by site-directed mutagenesis into the cysteine-free subtilisin-like enzyme from Bacillus lentus, i.e. Savinase. The free cysteine affects the enzyme activity only slightly but renders it sensitive to mercurials presumably due to an indirect effect. The results indicate that the -SH group is not involved in catalysis.
Surface pretreated low-temperature aluminum–aluminum wafer bonding (2017)

Aluminum–aluminum wafer bonding is becoming increasingly important in the production of CMOS microelectromechanical systems. So far, successful bonding has required extreme processing temperatures of 450 °C or more, because the chemically highly stable oxide layer acts as a diffusion barrier between the two aluminum metallization layers. By using the ComBond® system, in which a surface treatment and subsequent wafer bonding are both performed in a high vacuum cluster, for the first time successful Al–Al wafer bonding was possible at a temperature of 150 °C. The bonded interfaces were characterized using C-mode scanning acoustic microscopy and transmission electron microscopy, and featured areas of oxide-free, atomic contact.
Improving an inkjet printer: saturation enhancement based on segmentation and hue (2021)

In one of our previous paper [1] proposed in the last year, we described the color management pipeline that applied to our nail inkjet printer. However, the resulting prints are not as vivid as we would like to have since those prints are not well saturated. In this paper, we propose a saturation enhancement method based on the image segmentation and hue angle. This method will not necessarily give us the closest representation of the colors within the input image but could give us more saturated prints. The main idea that we perform our saturation enhancement method is to keep the lightness and hue constant, while stretching the chroma component.
ChemInform Abstract: A New Family of Highly Emissive Soluble Poly(p‐phenylene vinylene) Derivatives. A Step Toward Fully Conjugated Blue‐Emitting Poly(p‐phenylene vinylenes). (1998)

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.
Rethinking global digital health and AI-for-health innovation challenges (2023)

Digital health technologies can help tackle challenges in global public health. Digital and AI-for-Health Challenges, controlled events whose goal is to generate solutions to a given problem in a defined period of time, are one way of catalysing innovation. This article proposes an expanded investment framework for Global Health AI and digitalhealth Innovation that goes beyond traditional factors such as return on investment. Instead, we propose non monetary and non GDP metrics, such as Disability Adjusted Life Years or achievement of universal health coverage. Furthermore, we suggest a venture building approach around global health, which includes filtering of participants to reduce opportunity cost, close integration of implementation scientists and an incubator for the long-term development of ideas resulting from the challenge. Finally, we emphasize the need to strengthen human capital across a range of areas in local innovation, implementation-science, and in health services.
Quantifying the Impact of Research on Matching into Ophthalmology Residency (2018)

Purpose This article aims to quantify the impact of research on matching into various tiers of ophthalmology residency programs. Design In this study, 340 applicants who matriculated into ophthalmology residency programs in the United States from the class of 2019 were included. Data variables collected for each applicant composed of the following: Hirsch's index (h-index), total number of publications, journal impact factor, type of publication, and number of publications relating to ophthalmology. The primary outcome was tier of ophthalmology program that each applicant matched into, which was determined by two metrics: (1) the h-index of the department's faculty and (2) overall reputation of the residency program as characterized by the U.S. News and World Report Ophthalmology Rankings. Results After multivariate analysis, only the h-index was found to be associated with an increased likelihood of matching at a higher tier program when measuring tier based on the metric of institutional research output (p &lt; 0.0001). However, no research variable was found to be significant on multivariate analysis when assessing the impact of research on matching into a certain tier program based on reputation. The h-index was noted to increase by 1 for every 3.1 papers as the first author, every 4.9 years since the first publication, every 6.4 ophthalmology-related publications, and every publication in a journal with an impact factor of 5.2. Conclusion A higher applicant h-index is associated with matching at an ophthalmology program with greater research output; however, it is not associated with reputation of residency program.
Arginine-dependent hypusination of the eukaryotic translation initiation factor (eIF)5A drives erythroid lineage differentiation (2022)

Metabolic programs contribute to hematopoietic stem and progenitor cell (HSPC) fate but it is not known whether the metabolic regulation of protein synthesis controls HSPC differentiation. We discovered that SLC7A1/CAT1-dependent arginine uptake and its catabolism to spermidine control the erythroid specification of HSPCs via activation of eukaryotic translation initiation factor 5A (eIF5A). eIF5A activity is dependent on the metabolism of spermidine to hypusine and inhibiting hypusine synthesis abrogates erythropoiesis and diverts EPO-stimulated HSPCs to a myeloid fate. Proteomic profiling reveals mitochondrial translation to be a critical target of hypusinated eIF5A and induction of mitochondrial function partially rescues erythropoiesis in the absence of hypusine. Within the hypusine network, ribosomal proteins are highly enriched and we identify defective eIF5A hypusination in erythroid pathologies caused by abnormal ribosome biogenesis. Thus, eIF5A-dependent protein synthesis is critical in the branching of erythro-myeloid differentiation and attenuated eIF5A activity characterizes ribosomal protein-linked disorders of ineffective erythropoiesis.
[Alpha interferon induced hyperthyroidism: a case report and review of the literature]. (2015)

Treatment with alpha interferon in hepatitis C triggers a thyroid autoimmunity in a variable percentage of cases (2-8%). This complication raises some questions about its screening, the possibility to continue anti-viral therapy and thyroid treatment. Alpha interferon has an immunomodulatory effect on the thyroid, but also an inhibitory effect on thyroid hormone synthesis. This explains the occurrence of cases of thyroid dysfunction, which often remain undetected because of their latency. Factors predicting thyroid dysfunction with interferon use are: female sex, history of thyroid disease and previous autoimmunity. Several clinical aspects are encountered including hypothyroidism (the most frequent depending on the series) and hyperthyroidism related to Graves' disease. For their detection, a cooperation between general practionners, gastroenterologists and endocrinologists is mandatory thyroid function tests are requested before, during and after treatment,with alpha interferon. Therapeutic aspects of thyroid disorders range from simple monitoring to symptomatic treatment, such as thyroxine prescription in the presence of hypothyroidism. Antithyroid drugs radioactive iodine or thyroid surgery are used in cases of severe or persistent Graves' disease induced by alpha interferon.
Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement (2008)

Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate that researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate preduplication genome. In agreement with previous reports, we identify two WGD events in early vertebrates and another in teleost fish. However, we find that the early vertebrate WGD events were not followed by increased rates of genome rearrangement. Indeed, we measure massive genome rearrangement prior to these WGD events. We propose that the vertebrate WGD events may have been symptoms of a preexisting predisposition toward genomic structural change.
Thalamic Resting-State Functional Networks: Disruption in Patients with Mild Traumatic Brain Injury (2011)

These findings of abnormal thalamic RSNs lend further support to the presumed subtle thalamic injury in patients with MTBI. Resting-state functional MR imaging can be used as an additional imaging modality for detection of thalamocortical connectivity abnormalities and for better understanding of the complex persistent postconcussive syndrome.
Design of Substituted Imidazolidinylpiperidinylbenzoic Acids as Chemokine Receptor 5 Antagonists: Potent Inhibitors of R5 HIV-1 Replication (2013)

The redesign of the previously reported thiophene-3-yl-methyl urea series, as a result of potential cardiotoxicity, was successfully accomplished, resulting in the identification of a novel potent series of CCR5 antagonists containing the imidazolidinylpiperidinyl scaffold. The main redesign criteria were to reduce the number of rotatable bonds and to maintain an acceptable lipophilicity to mitigate hERG inhibition. The structure-activity relationship (SAR) that was developed was used to identify compounds with the best pharmacological profile to inhibit HIV-1. As a result, five advanced compounds, 6d, 6e, 6i, 6h, and 6k, were further evaluated for receptor selectivity, antiviral activity against CCR5 using (R5) HIV-1 clinical isolates, and in vitro and in vivo safety. On the basis of these results, 6d and 6h were selected for further development.
In vivo characterization of emerging SARS-CoV-2 variant infectivity and human antibody escape potential (2021)

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads, variants with enhanced virulence and transmissibility have emerged. Although in vitro systems allow rapid characterization, they do not fully recapitulate the dynamic interaction of virions and neutralizing antibodies in the airway. Here, we demonstrate that the N501Y variant permits respiratory infection in unmodified mice. We utilize N501Y to survey in vivo pseudovirus infection dynamics and susceptibility to reinfection with the L452R (Los Angeles), K417N + E484K (South Africa), and L452R + K417N + E484Q (India) variants. Human coronavirus disease 2019 (COVID-19)+ or vaccinated antibody isotypes, titers, variant receptor binding domain (RBD) binding, and neutralization potential are studied, revealing numerous significant correlations. Immune escape of the K417N + E484K variant is observed because infection can be appreciated in the nasopharynx, but not lungs, of mice transferred with low-antibody-tier plasma. Conversely, near-complete protection is observed in animals receiving high-antibody-tier plasma, a phenomenon that can only be appreciated in vivo.
How to analyse relaxation and leakage currents of dielectric thin films: Simulation of voltage-step and voltage-ramp techniques (1995)

Abstract An empirical electrical equivalent circuit for dielectric thin films, based on experimental data, is developed. Current responses to voltage-steps and to voltage-ramps are calculated and compared with experimental data. The simulation allows us to separate current contributions of different physical processes while the experiment only reveals the sum of the currents.
LOX-1 Deletion Attenuates Myocardial Fibrosis in the Aged Mice, Particularly Those With Hypertension (2021)

<b>Background:</b> Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is a transmembrane glycoprotein that mediates uptake of oxidized low-density lipoprotein (ox-LDL) into cells. Previous studies had shown that LOX-1 deletion had a potential to inhibit cardiac fibrosis in mouse models of hypertension and myocardial infarction. Whether LOX-1 deletion also affects cardiac fibrosis associated with aging still remains unknown. The aim of this study was to investigate the effect of LOX-1 deletion on myocardial fibrosis in the aged mice. <b>Methods:</b> C57BL/6 mice and LOX-1 knockout (KO) mice with C57BL/6 background were studied to the age of 60 weeks. Both genotypes of aged mice were exposed to angiotensin II (Ang II) or saline for additional 4 weeks. The mice were then sacrificed, and myocardial fibrosis, reactive oxygen species (ROS) and expression of LOX-1, fibronectin, collagens, p22<sup>phox</sup>, and gp91<sup>phox</sup> were measured. <b>Results:</b> LOX-1 deletion markedly reduced Ang II-mediated rise of blood pressure in the aged mice (vs. saline-treated mice). LOX-1 deletion also limited fibrosis and decreased fibronectin and collagen-3 expression in the hearts of aged mice, but not the expression of collagen-1 and collagen-4. LOX-1 deletion also inhibited ROS production and p22<sup>phox</sup> expression. As the aged mice were exposed to Ang II for 4 weeks (resulting in hypertension), LOX-1 deletion more pronounced inhibiting myocardial fibrosis and ROS production, and decreasing expression of fibronectin, collagen-1, collagen-2, collagen-3, p22<sup>phox</sup>, and gp91<sup>phox</sup>. <b>Conclusion:</b> LOX-1 deletion limited fibrosis and ROS production in the hearts of aged mice. This effect was more pronounced in the aged mice with hypertension induced by Ang II infusion.
Enhanced Integrin α4β1–Mediated Adhesion Contributes to a Mobilization Defect of Endothelial Progenitor Cells in Diabetes (2016)

Diabetes is associated with a deficit of circulating endothelial progenitor cells (EPCs), which has been attributed to their defective mobilization from the bone marrow. The basis for this mobilization defect is not completely understood, and we sought to determine if hyperglycemic conditions enhanced EPC adhesion. We found that culturing EPCs in high glucose media increased adhesion to bone marrow stromal cells. This enhanced adhesion was associated with decreased expression of protein kinase A regulatory subunit 1β (PRKAR1β), activation of protein kinase A (PKA), and phosphorylation of α4-integrin on serine 988. This potentiated adhesion was reversed by treatment with a PKA inhibitor, overexpression of PRKAR1β, or expression of a phosphorylation-defective α4-integrin variant (α4[S988A]). Using a model of type 1 diabetes, we showed that α4(S988A)-expressing mice have more circulating EPCs than their wild-type counterparts. Moreover, diabetic α4(S988A) mice demonstrate enhanced revascularization after hind limb ischemia. Thus, we have identified a novel signaling mechanism activating PKA in diabetes (downregulation of an inhibitory regulatory subunit) that leads to deficits of circulating EPCs and impaired vascular repair, which could be reversed by α4-integrin mutation.
PIFT (2016)

Phones today carry sensitive information and have a great number of ways to communicate that data. As a result, malware that steal money, information, or simply disable functionality have hit the app stores. Current security solutions for preventing undesirable data leaks are mostly high-overhead and have not been practical enough for smartphones. In this paper, we show that simply monitoring just some instructions (only memory loads and stores) it is possible to achieve low overhead, highly accurate information flow tracking. Our method achieves 98% accuracy (0% false positive and 2% false negative) over DroidBench and was able to successfully catch seven real-world malware instances that steal phone number, location, and device ID using SMS messages and HTTP connections.
Risks of Cracking and Delamination in Patch Repair (2002)

The durability of concrete repair may be measured in terms of its resistance to cracking and to ingress by aggressive species. This paper addresses the various issues that form the nucleus of cracking resistance, including the role of material parameter indices such as free drying shrinkage and specific tensile creep. Data for these indices are presented for two new generation repair materials, and attention is drawn to the inherent anomalies existing in international specifications for shrinkage measurement. The paper concludes by defining risk factors associated with the probability of failure of a patch repair in one of three identified modes. The risk factors are computed for a patch repair using a rigid substrate idealization, and the probability of failure in cracking, delamination, or peeling modes is assessed.
Research Resource: Diagnostic and Therapeutic Potential of Nuclear Receptor Expression in Lung Cancer (2012)

Lung cancer is the leading cause of cancer-related death. Despite a number of studies that have provided prognostic biomarkers for lung cancer, a paucity of reliable markers and therapeutic targets exist to diagnose and treat this aggressive disease. In this study we investigated the potential of nuclear receptors (NRs), many of which are well-established drug targets, as therapeutic markers in lung cancer. Using quantitative real-time PCR, we analyzed the expression of the 48 members of the NR superfamily in a human panel of 55 normal and lung cancer cell lines. Unsupervised cluster analysis of the NR expression profile segregated normal from tumor cell lines and grouped lung cancers according to type (i.e. small vs. non-small cell lung cancers). Moreover, we found that the NR signature was 79% accurate in diagnosing lung cancer incidence in smokers (n = 129). Finally, the evaluation of a subset of NRs (androgen receptor, estrogen receptor, vitamin D receptor, and peroxisome proliferator-activated receptor-γ) demonstrated the therapeutic potential of using NR expression to predict ligand-dependent growth responses in individual lung cancer cells. Preclinical evaluation of one of these receptors (peroxisome proliferator activated receptor-γ) in mouse xenografts confirmed that ligand-dependent inhibitory growth responses in lung cancer can be predicted based on a tumor's receptor expression status. Taken together, this study establishes NRs as theragnostic markers for predicting lung cancer incidence and further strengthens their potential as therapeutic targets for individualized treatment.
Solution‐Processed HafSOx and ZircSOx Inorganic Thin‐Film Dielectrics and Nanolaminates (2007)

Abstract New thin‐film dielectrics and nanolaminates have been synthesized via aqueous‐solution deposition of Hf and Zr sulfates, where facile gelation and vitrification of the precursor solution have been achieved without organic additives. X‐ray reflectivity, imaging, and metal‐insulator‐metal capacitor performance reveal that smooth, atomically dense films are readily produced by spin coating and modest thermal treatment ( T &lt; 325 °C). Dielectric characteristics include permittivities covering the range of 9–12 with breakdown fields up to 6 MV cm –1 . Performance as gate dielectrics is demonstrated in field‐effect transistors exhibiting small gate‐leakage currents and qualitatively ideal device performance. The low‐temperature processing, uniformity, and pore‐free nature of the films have also allowed construction of unique, high‐resolution nanolaminates exhibiting individual layers as thin as 3 nm.
Computing the liquid crystal director field in optical phased arrays (2004)

Optical phased arrays using birefringent liquid crystals can efficiently steer a laser communication beam to a small angle. The algorithm presented derives a thickness for the liquid crystal cell and computes a sequence of voltages for the device electrodes that best deflects the beam.
Reasoning about many-to-many requirement relationships in spreadsheets (2003)

To help improve the reliability of spreadsheets created by end users, we are working to allow users to communicate the purpose and other underlying information about their spreadsheets, using a form of requirement specifications we call "guards." For large spreadsheets with replicated/shared formulas across groups of rows or columns, guards can only be practical if users can enter them across these groups of rows or columns. The problem is, this introduces many-to-many relationships, and it is not clear how the system should reason and communicate about them in a way that will make sense to end users. In this paper, we present the human-centric design rationale for our approach to how the system should reason about such many-to-many relationships. The design decisions are presented with their reasons gleaned from two design-time models - cognitive dimensions and attention economics -and from the users themselves in a small think-aloud study.
Tractable Identification of Electric Distribution Networks (2023)

The identification of distribution network topology and parameters is a critical problem that lays the foundation for improving network efficiency, enhancing reliability, and increasing its capacity to host distributed energy resources. Network identification problems often involve estimating a large number of parameters based on highly correlated measurements, resulting in an ill-conditioned and computationally demanding estimation process. We address these challenges by proposing two admittance matrix estimation methods. In the first method, we use the eigendecomposition of the admittance matrix to generalize the notion of stationarity to electrical signals and demonstrate how the stationarity property can be used to facilitate a maximum a posteriori estimation procedure. We relax the stationarity assumption in the second proposed method by employing Linear Minimum Mean Square Error (LMMSE) estimation. Since LMMSE estimation is often ill-conditioned, we introduce an approximate well-conditioned solution based on eigenvalue truncation. Our quantitative results demonstrate the improvement in computational efficiency compared to the state-of-the-art methods while preserving the estimation accuracy.