gebhart/patrepeval huggingface dataset:
Phospho-Serine-118 Estrogen Receptor-α Detection in Human Breast Tumors in Vivo (2004)

P-Ser(118)-ERalpha detection is associated with a more differentiated phenotype and other markers of good prognosis in human breast cancer. P-Ser(118)-ERalpha is correlated with active MAPK in human breast tumor biopsies, suggesting the possibility that active MAPK either directly or indirectly has a role in the regulation of P-Ser(118)-ERalpha expression in vivo. These data provide evidence for a role of P-Ser(118)-ERalpha in human breast cancer in vivo.
Leaf Water Status from Lab Estimates of VIS-NIR Reflectance and Transmittance (2018)

Remotely sensing the water status of plant canopies remains a long term goal of remote sensing research. Established approaches involve measurements in the thermal infrared and the 900-2000nm reflective infrared. Less popular UV-visible-NIR techniques presumably deserve research attention, because photochemical changes linked to plant water status manifest spectral light scattering and absorption changes. Here we estimated the visible and NIR light reflected from the leaf interior and the leaf transmittance of corn (Zea mays L.) leaves having a range of relative water contents. Our results highlight the importance of both scattering effects and effects due to absorption by leaf pigments.
A High Gain Antenna With an Optimized Metamaterial Inspired Superstrate (2012)

A metamaterial unit cell with a low refractive index over a wide frequency band is proposed and designed. The effective material parameters of the unit cell are extracted, and the unit cell forms a planar three-layer metamaterial structure used as a superstrate for broadside gain enhancement of a patch antenna at 10 GHz. The proposed superstrate is optimized along with the antenna to enhance its beam-focusing ability, taking into account the oblique wave incidence from the radiation source. Both simulation and measurement of the antenna with the optimized superstrate show that this configuration is able to achieve a broadside gain 70%–80% of the maximum gain from the ideal effective radiation surface.
Determination of a Solvent Hydrogen-Bond Acidity Scale by Means of the Solvatochromism of Pyridinium-N-phenolate Betaine Dye 30 and PCM-TD-DFT Calculations (2014)

Empirical parameters of solvents describing their hydrogen-bond (HB) acidity (e.g., the Kamlet-Taft α parameter) are often difficult to determine for new solvents because they are not directly related to a single definition process. Here, we propose a simple method based on one probe, the betaine dye 30, and one reference process, the solvatochromism of this dye, measured by its first electronic transition energy, ET(30). These ET(30) values are calculated within the time-dependent density functional theory framework, using a polarizable continuum solvent model (PCM). The part of ET(30) values that is not included in the PCM calculation is taken as the HB component of the measured ET(30) values, allowing us to deduce a solvent HB acidity parameter α1. The validity of this simple model is assessed by good linear correlations between α1 and a variety of solute properties mainly depending on the solvent's HB acidity. The quality of fit observed with α1 is at least comparable with that obtained by previous solvent HB acidity scales. The simplicity of our method is illustrated by the determination of α1 and of its companion, the electrostatic solvent parameter ES, for some new green solvents derived from glycerol.
Discoidin Domain Receptor 2 Interacts with Src and Shc following Its Activation by Type I Collagen (2002)

Discoidin domain receptor 2 (DDR2) is an unusual receptor tyrosine kinase in that its ligand is fibrillar collagen rather than a growth factor-like peptide. We examined signal transduction pathways of DDR2. Here we show that DDR2 is also unusual in that it requires Src activity to be maximally tyrosine-phosphorylated, and that Src activity also promotes association of DDR2 with Shc. The interaction with Shc involves a portion of Shc not previously implicated in interaction with receptor tyrosine kinases. These results identify Src kinase and the adaptor protein Shc as key signaling intermediates in DDR2 signal transduction. Furthermore, Src is required for DDR2-mediated transactivation of the matrix metalloproteinase-2 promoter. The data support a model in which Src and the DDR2 receptor cooperate in a regulated fashion to direct the phosphorylation of both the receptor and its targets.
Efficient replica maintenance for distributed storage systems (2006)

This paper considers replication strategies for storage systems that aggregate the disks of many nodes spread over the Internet. Maintaining replication in such systems can be prohibitively expensive, since every transient network or host failure could potentially lead to copying a server's worth of data over the Internet to maintain replication levels. The following insights in designing an efficient replication algorithm emerge from the paper's analysis. First, durability can be provided separately from availability; the former is less expensive to ensure and a more useful goal for many wide-area applications. Second, the focus of a durability algorithm must be to create new copies of data objects faster than permanent disk failures destroy the objects; careful choice of policies for what nodes should hold what data can decrease repair time. Third, increasing the number of replicas of each data object does not help a system tolerate a higher disk failure probability, but does help tolerate bursts of failures. Finally, ensuring that the system makes use of replicas that recover after temporary failure is critical to efficiency. Based on these insights, the paper proposes the Carbonite replication algorithm for keeping data durable at a low cost. A simulation of Carbonite storing 1 TB of data over a 365 day trace of PlanetLab activity shows that Carbonite is able to keep all data durable and uses 44% more network traffic than a hypothetical system that only responds to permanent failures. In comparison, Total Recall and DHash require almost a factor of two more network traffic than this hypothetical system.
Identification of Key Actor Nodes: A Centrality Measure Ranking Aggregation Approach (2022)

The identification of key actors in complex networks has gathered significant interest by virtue of their importance in modern applications. Several of the existing methods employ standard centrality measures to achieve their goal and as a result, one of the main challenges is identifying key actor nodes with high relevance across all such measures. In this work, we propose a model based on the use of graph convolutional networks (GeNs) that retrieves the key actors in a network based on a centrality measure ranking aggregation scheme. We experimentally demonstrate the effectiveness of our solution compared to baseline and state-of-the-art approaches in terms of: i) accuracy, ii) performance compared to standard machine learning approaches, and iii) influence propagation capabilities.
Coding sequences of sarcoplasmic reticulum calcium ATPase regulatory peptides and expression of calcium regulatory genes in recurrent exertional rhabdomyolysis (2019)

The SLN gene encodes a uniquely truncated peptide in the horse versus other species. Variants in the coding sequence of SLN, MLRN, or DWORF were not associated with RER. Males with RER have differential gene expression that could reflect adaptations to stabilize RYR1.
Maternal deprivation induces alterations in cognitive and cortical function in adulthood (2018)

Early life trauma is a risk factor for a number of neuropsychiatric disorders, including schizophrenia (SZ). The current study assessed how an early life traumatic event, maternal deprivation (MD), alters cognition and brain function in rodents. Rats were maternally deprived in the early postnatal period and then recognition memory (RM) was tested in adulthood using the novel object recognition task. The expression of catechol-o-methyl transferase (COMT) and glutamic acid decarboxylase (GAD67) were quantified in the medial prefrontal cortex (mPFC), ventral striatum, and temporal cortex (TC). In addition, depth EEG recordings were obtained from the mPFC, vertex, and TC during a paired-click paradigm to assess the effects of MD on sensory gating. MD animals exhibited impaired RM, lower expression of COMT in the mPFC and TC, and lower expression of GAD67 in the TC. Increased bioelectric noise was observed at each recording site of MD animals. MD animals also exhibited altered information theoretic measures of stimulus encoding. These data indicate that a neurodevelopmental perturbation yields persistent alterations in cognition and brain function, and are consistent with human studies that identified relationships between allelic differences in COMT and GAD67 and bioelectric noise. These changes evoked by MD also lead to alterations in shared information between cognitive and primary sensory processing areas, which provides insight into how early life trauma confers a risk for neurodevelopmental disorders, such as SZ, later in life.
Jack-up reinstallation near a footprint cavity (2010)

Jack-up units are self-elevating mobile platforms that are extensively used in the offshore oil and gas industry. On removal of the jack-up unit, the legs are retracted from the seabed leaving depressions at the site. During jack-up reinstallation near these footprints, eccentric and/or inclined loading conditions may occur, inducing large displacements and/or forces in the jack-up legs. If the total forces exceeded the structural capacity, there may be damage in the jack-up leg and at worst could lead to collapse of the rig.
Data from Exposure–Response of Veliparib to Inform Phase II Trial Design in Refractory or Relapsed Patients with Hematological Malignancies (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; A phase I trial of veliparib in combination with topotecan plus carboplatin (T+C) demonstrated a 33% objective response rate in patients with hematological malignancies. The objective is to perform exposure–response analysis to inform the phase II trial design.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Pharmacokinetic, efficacy, and safety data from 95 patients, who were administered 10 to 100 mg b.i.d. doses of veliparib for either 8, 14, or 21 days with T+C, were utilized for exposure–efficacy (objective response and overall survival) and exposure–safety (≥grade 3 mucositis) analysis. Multivariate cox proportional hazards and logistic regression analyses were conducted. The covariates evaluated were disease status, duration of treatment, and number of prior therapies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The odds of having objective response were 1.08-fold with 1,000 ng/hr/mL increase in AUC, 1.8-fold with &gt;8 days treatment, 2.8-fold in patients with myeloproliferative neoplasms (MPN), and 0.5-fold with ≥2 prior therapies. Based on analysis of overall survival, hazard of death decreased by 1.5% for 1,000 ng/hr/mL increase in AUC, 39% with &gt;8 days treatment, 44% in patients with MPN, while increased by 19% with ≥2 prior therapies. The odds of having ≥grade 3 mucositis increased by 29% with 1,000 ng.h/mL increase in AUC.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Despite shallow exposure–efficacy relationship, doses lower than 80 mg do not exceed veliparib single agent preclinical IC&lt;sub&gt;50&lt;/sub&gt;. Shallow exposure–mucositis relationship also supports the 80-mg dose. Based on benefit/risk assessment, veliparib at a dose of 80 mg b.i.d. for at least 14 days in combination with T+C is recommended to be studied in MPN patients. &lt;i&gt;Clin Cancer Res; 23(21); 6421–9. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
A Controllable Self‐Assembly Method for Large‐Scale Synthesis of Graphene Sponges and Free‐Standing Graphene Films (2010)

Abstract A simple method to prepare large‐scale graphene sponges and free‐standing graphene films using a speed vacuum concentrator is presented. During the centrifugal evaporation process, the graphene oxide (GO) sheets in the aqueous suspension are assembled to generate network‐linked GO sponges or a series of multilayer GO films, depending on the temperature of a centrifugal vacuum chamber. While sponge‐like bulk GO materials (GO sponges) are produced at 40 °C, uniform free‐standing GO films of size up to 9 cm 2 are generated at 80 °C. The thickness of GO films can be controlled from 200 nm to 1 µm based on the concentration of the GO colloidal suspension and evaporation temperature. The synthesized GO films exhibit excellent transparency, typical fluorescent emission signal, and high flexibility with a smooth surface and condensed density. Reduced GO sponges and films with less than 5 wt% oxygen are produced through a thermal annealing process at 800 °C with H 2 /Ar flow. The structural flexibility of the reduced GO sponges, which have a highly porous, interconnected, 3D network, as well as excellent electrochemical properties of the reduced GO film with respect to electrode kinetics for the [Fe(CN) 6 ] 3−/4− redox system, are demonstrated.
Fighting Spam by Breaking the Econonmy of Advertisment by Unsolicited Emails (2015)

Unsolicited email (spam) is still a problem for users of the email service. Even though current email anti-spam solutions filter most spam emails, some spam emails still are delivered to the inbox of users. A special class of spam emails advertises websites, e.g., online dating sites or online pharmacies. The success rate of this kind of advertisement is rather low, however, as sending an email does only involve minimal costs, even a very low success rate results in enough revenue such that this kind of advertisement pays off. The anti-spam approach presented in this paper aims on increasing the costs for websites that are advertised by spam emails and on lowering the revenues from spam. Costs can be increased for a website by increasing traffic. Revenues can be decreased by making the website slow responding, hence some business gets lost. To increase costs and decreased revenues a decentralized peer-to-peer coordination mechanism is used to have mail clients to agree on a start date and time for an anti-spam campaign. During a campaign, all clients that received spam emails advertings a website send an opt-out request to this website. A huge number of opt-out requests results in increased traffic to this website and will likely result in a slower responsibility of the website. The coordination mechanism presented in this paper is based on a peer-to-peer mechanisms and a so-called paranoid trust model to avoid manipulation by spammers. An implementation for the Thunderbird email client exist. The anti-spam approach presented in this paper breaks the economy of spam, hence makes advertisement by unsolicited emails unattractive.
Use of Insulin Lispro in the Outpatient Management of Ketonuria (1998)

These data indicate that insulin lispro is an effective option for the outpatient management of ketonuria.
Influence of mineral or polymeric modification on bentonite-based tunnel face support (2021)

The time-dependent penetration of bentonite-based support fluids into non-cohesive soil is a current subject of investigation, especially in the field of shield tunnelling with fluid face support due to the cyclic excavation process. Research has so far focused on linking the time-dependent penetration of clean bentonite suspensions with the penetration rate of the cutting wheel. However, experience shows that bentonite slurries in-situ often contain suspended fines, which can change the penetration behaviour of the slurry significantly. Moreover, in recent years, it has become common practice to improve stability or rheological behaviour of bentonite suspensions by adding water-soluble polymers. Understanding the effect of such slurry modifications on the time-dependent penetration behaviour is an essential basis for realistic face support models. The present study analyses the influence of a mineral or polymeric modification of a typical bentonite slurry by means of penetration tests with sand columns at over-pressure. The sand type was chosen so that a pure unmodified bentonite slurry does not create an external filter cake, but penetrates into the pore space of the soil to be supported. Pore water pressure sensors along the height and measurements of inflow and outflow using electronic balances enable a time-dependent determination of penetration depth and pressure transfer. For selected tests, a special focus lies on the evaluation of the effect of filter cake formed and penetration on the soil permeability. From the results, it can be concluded that a bentonite modification with fines results in a significant reduction in the penetration depth with the formation of an external filter cake. The addition of specific polymers reduces the amount of bentonite needed to create a stable suspension with defined rheology. Special care must be taken regarding the choice of fines and polymers.
Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance (2020)

Abstract Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops. Summary statement Lowland rice varieties Hacha and Lachit were selected for contrasting abilities to cope with iron excess stress. Morphological and physiological phenotypes were mirrored by molecular transcriptome changes, indicating altered metal homeostasis in the root as an adaptive tolerance mechanism in Lachit.
RNA-binding proteins of bovine rotavirus (1986)

Two major bovine rotavirus proteins have RNA-binding activity as shown by an RNA overlay-protein blot assay. Of the six proteins in purified virions, only one showed RNA-binding activity. This 92,000-molecular-weight (92K) protein was present in both single- and double-shelled particles. Its RNA-binding activity was blocked by preincubation with monospecific antibody to VP2. Thus, the 92K RNA-binding protein in rotavirus virions is VP2, the second most abundant protein in single-shelled particles. In infected cell extracts, numerous cellular RNA-binding proteins and two virus-specific RNA-binding proteins were detected, VP2 and a 31K nonstructural (NS31) protein. VP2 bound single-stranded RNA in preference to double-stranded RNA, whereas NS31 bound both single- and double-stranded RNA equally well. Binding did not appear to be nucleotide sequence specific, because RNA from uninfected cells and an unrelated RNA virus bound to VP2 and to NS31 as did rotavirus RNA. This technique showed that both cellular and rotavirus RNA-binding proteins also bound DNA. VP2 interacted with rotavirus RNA over a broad pH range, with an optimum at pH 6.4 to 6.8, and at NaCl concentrations between 0 and 100 mM. The RNA-binding activity of NS31 exhibited similar pH and NaCl dependency. Sequence-specific nucleic acid binding could be detected by this method. When labeled synthetic oligodeoxyribonucleotides corresponding to the 3' and 5' plus-sense terminal sequences of rotavirus gene segments were used as probes, the 3' synthetic oligodeoxyribonucleotide bound to one 48K protein in control and infected cells. This suggests that there may be a specific functional interaction between the 48K cellular protein and this 3'-terminal noncoding region of the rotavirus genome or mRNA. These data show that the RNA overlay-protein blot assay is a useful test to identify some cellular and viral proteins with RNA-binding activity. For bovine rotavirus, the evidence suggests that, of all the virus-specific proteins, VP2 and NS31 are most likely to interact with RNA during transcription and replication or virus assembly or both.
Supplementary Data from Bioinformatically Expanded Next-Generation Sequencing Analysis Optimizes Identification of Therapeutically Relevant <i>MET</i> Copy Number Alterations in >50,000 Tumors (2023)

Supplementary Data from Bioinformatically Expanded Next-Generation Sequencing Analysis Optimizes Identification of Therapeutically Relevant &lt;i&gt;MET&lt;/i&gt; Copy Number Alterations in &gt;50,000 Tumors
Comportamiento de estructuras fotónicas de computación aptas en comunicaciones ópticas (2003)

Cuando se introduce una no linealidad optica dentro de una cavidad resonante, se pueden producir efectos de conmutacion rapida entre dos estados diferenciados de transmision. Este fenomeno se conoce por biestabilidad optica, caracterizado porque la salida de los dispositivos con este tipo de comportamiento constan de dos estados estables diferenciados y una region asociada a un ciclo de histeresis en la cual el sistema es inestable. En dicha region la salida posee valores diferentes para un mismo valor de entrada en funcion de la historia del dispositivo.
Stable Fabrication of High Breakdown Voltage Mesa-Structure Vertical GaN p-n Junction Diodes Using Electrochemical Etching (2018)

A wet etching has been performed using an electrochemical etching method to fabricate mesa-structure vertical GaN p-n junction diodes. In case of conventional dry etching, the breakdown voltages of the p-n diodes showed scattered values probably due to local concentration of electric field by roughness at the side wall of the mesa. Smooth and damage-free surface have been obtained by the wet etching, which has enabled higher and stable the breakdown voltages.
3D-Mesa “Bridge” Silicon Microdosimeter: Charge Collection Study and Application to RBE Studies in $^{12}{\rm C}$ Radiation Therapy (2015)

Microdosimetry is an extremely useful technique, used for dosimetry in unknown mixed radiation fields typical of space and aviation, as well as in hadron therapy. A new silicon microdosimeter with 3D sensitive volumes has been proposed to overcome the shortcomings of the conventional Tissue Equivalent Proportional Counter. In this article, the charge collection characteristics of a new 3D mesa microdosimeter were investigated using the ANSTO heavy ion microprobe utilizing 5.5 MeV He <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2+</sup> and 2 MeV H <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> ions. Measurement of the microdosimetric characteristics allowed for the determination of the Relative Biological Effectiveness of the <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> C heavy ion therapy beam at the Heavy Ion Medical Accelerator in Chiba (HIMAC), Japan. Well-defined sensitive volumes of the 3D mesa microdosimeter have been observed and the microdosimetric RBE obtained showed good agreement with the TEPC. The new 3D mesa “bridge” microdosimeter is a step forward towards a microdosimeter with fully free-standing 3D sensitive volumes.