gebhart/patrepeval huggingface dataset:
Growth of embedded photonic crystals for GaN-based optoelectronic devices (2009)

We present three different techniques to fabricate embedded photonic crystals in GaN-based structures by metal organic chemical vapor deposition, geared toward high efficiency and high directionality light emitting diodes. Compared to the usual lateral epitaxial overgrowth, the novelty lies in the very short grating periods (varying from 180 to 350 nm) and the two-dimensional triangular nature of the grating. Coalescence was obtained over air-gap photonic crystals with thicknesses down to 70 nm, an essential requirement to obtain an efficient interaction between the optical guided modes and the photonic crystals. The quality and surface morphology of the overgrown layers were assessed by transmission electron microscopy and atomic force microscopy measurements. The thin coalesced GaN layer presented a fairly smooth surface (rms roughness of 1.27 nm for a 20×20 μm2 scan) with no extra defects created by the embedded photonic crystals.
Abstract 2093: Imaging single cell drug target engagement in vivo reveals heterogeneous fractional occupancy (2016)

Abstract To produce effective therapeutic treatment, drugs need to reach and engage the cognate target in the cells of interest. Incomplete target occupancy may lead to cell survival and disease progression. Therefore, for maximum efficacy, it is critical to achieve high target occupancy within each cell of a tumor. However, the tumor microenvironment likely creates a dynamic, heterogenous distribution of drug that limits target occupancy in some cells. Unfortunately, we lack the tools to determine target engagement at the cellular level, which prevents studies on heterogeneous target occupancy and contributes to the poor understanding of drug failure mechanisms. Here, we developed an approach to measure target engagement of small molecule inhibitors within single cells in mouse xenograft in vivo tumor models. Our method uses fluorescently labeled, target specific companion imaging drugs, fluorescence polarization imaging, and intravital microscopy, to measure target occupancy of unlabeled, clinical drugs in single cells. We calculated the equivalent in vitro exposure of ibrutinib, a covalent BTK inhibitor, in vivo, but found increased cellular heterogeneity, highlighting differences between in vivo activity and in vitro measurements. Additionally, following systemic delivery of the reversible PARP inhibitor olaparib, we found cells with substantial uninhibited target when average measurements indicated all target was occupied, illustrating drug activity heterogeneity that may lead to tumor survival. These results demonstrate that our technique, which is the first to measure unlabeled drug engagement with target in single cells, can quantitate cellular fractional occupancy heterogeneity during drug treatment. We expect this approach to serve as a valuable tool when measuring cellular pharmacology in vivo, providing insight on dosing, drug activity in the tumor and sources of heterogeneous drug distribution. Citation Format: Matt Dubach, Ralph Weissleder. Imaging single cell drug target engagement in vivo reveals heterogeneous fractional occupancy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2093.
Functional Suppression by FoxP3+CD4+CD25highRegulatory T Cells during Acute Hepatitis C Virus Infection (2007)

Collectively, these data indicate that patients with acute HCV infection who develop chronicity versus spontaneous resolution exhibit temporal changes in T(reg) cell function. It is possible that repetitive viral antigenic stimulation alters the function of T(reg) cells over time.
Corrigendum to “Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitis” (J. Dairy Sci. 96:3611–3620) (2014)

Cicely Washington (Abbott Molecular-Athogen, Carlsbad, CA) was erroneously omitted as a co-author of this article. All authors agree to her addition as an author. The authors regret the error. Evaluation of PCR electrospray-ionization mass spectrometry for rapid molecular diagnosis of bovine mastitisJournal of Dairy ScienceVol. 96Issue 6PreviewBovine mastitis, an inflammatory disease of the mammary gland, is one of the most costly diseases affecting the dairy industry. The treatment and prevention of this disease is linked heavily to the use of antibiotics in agriculture and early detection of the primary pathogen is essential to control the disease. Milk samples (n = 67) from cows suffering from mastitis were analyzed for the presence of pathogens using PCR electrospray-ionization mass spectrometry (PCR/ESI-MS) and were compared with standard culture diagnostic methods. Full-Text PDF Open Archive
Crystal Structure of Bacillus anthracis Transpeptidase Enzyme CapD (2009)

Bacillus anthracis elaborates a poly-gamma-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the gamma-glutamyltranspeptidase CapD with and without alpha-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-gamma-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-gamma-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro(427), Gly(428), and Gly(429) activate the catalytic residue of the enzyme, Thr(352), and stabilize an oxyanion hole via main chain amide hydrogen bonds.
Integrative oncology consultations at a comprehensive cancer center: Analysis of patient reported outcomes. (2016)

e21690 Background: Patients (pts) receiving cancer care are increasingly interested in complementary health approaches. We report on demographics and patient reported outcomes in an integrative oncology (IO) clinic. Methods: Pts presenting for IO consultation or follow-up completed: Measure Yourself Concerns and Wellbeing (MYCaW), Edmonton Symptom Assessment Scale (ESAS), Short Form 12 (SF-12), and an overall satisfaction questionnaire. Consultations were provided by medical oncologists. Results: For 2,474 consultations from 9/2009 to 12/2013, 26.0% (n = 643) had ≥ 1 follow-up visit (mean 3.2; SD1.8). Most were female (69%) and white (75%); most frequent cancer types were breast (29%) and gastrointestinal (13%); 29% had advanced disease. Most common concerns (MYCaW) were Integrative Approach (34.2%), Herbs/Supplements (33.8%), and Nutrition (21.1%). At baseline, ESAS scores were highest for Sleep (4.2; SD 2.8), Fatigue (4.0; SD 2.8), Well-Being (3.8 SD 2.6) and Anxiety (3.1; SD 2.9). Mean standardized T-scores on the SF-12 (n = 1253) were physical health 35.3 and mental health 46.8 (50 = healthy populations). Older age, living locally, and higher levels of anxiety and psychological distress were predictors of follow up. For ESAS baseline scores ≥ 4 and follow up within 30 days of consultation, we observed overall improvement in symptoms (38-60% of pts with ESAS decrease ≥ 1). Integrative Approach, Herbs/Supplements, and Pain were most likely reasons for follow up. Integrative services accessed following the initial consultation included Acupuncture (n = 215 pts, mean 4.7 visits); Massage (n = 156, mean 4); Physical Therapy ( n = 75, mean 1.3); Meditation (n = 72, mean 1.3); Dietitian (n = 70, mean 1.1); and Music Therapy (n = 36, mean 1.8). Pts were satisfied to very satisfied with how well concern 1 (8, SD 2.2) and concern 2 (9.1, SD 1.8) were addressed. Overall satisfaction was high at both initial encounter (9.4; SD 1.3) and first follow up (9.5; SD 1.2). Conclusions: An IO consultation satisfactorily addressed patient concerns about an integrative approach and herbs/supplements, with significant improvements in symptom distress. Pts seen had a moderate symptom burden with lower than average physical health.
Supplementary Table 11 from Comprehensive Genome Methylation Analysis in Bladder Cancer: Identification and Validation of Novel Methylated Genes and Application of These as Urinary Tumor Markers (2023)

&lt;p&gt;XLS file - 19.4K&lt;/p&gt;
FP744WATER-SOLUBLE VITAMIN LEVELS AND OPTIMAL SUPPLEMENTATION IN CHRONIC ON-LINE HEMODIAFILTRATION PATIENTS (2019)

non-PEW group, the difference was insignificant (52.3169 vs 48.6768 kg respectively, p=0.129). MAC and MAMC were significantly higher in non-PEW group. SGA and MIS were also significantly higher in PEW group. Patients with PEW had significantly lower blood hemoglobin, serum albumin, creatinine and total cholesterol together with significantly higher serum ferritin than the non-PEW group. SF-12 Mental Composite was significantly higher in non-PEW group, while the other components of Quality of life (Symptom/ problem list, Effects of kidney disease, Burden of kidney disease as well as SF-12 Physical Composite) were not different between the two groups. CONCLUSIONS: PEW is not uncommon in HD patients. The risk of PEW increases considerably with longer HD duration.and is associated with lower macronutrient consumption. Compared to non-PEW, HD patients with PEW are more hydrated and had lower body fat mass. Anthropometric measurements seem to be expressive of muscle wasting in PEW patients. Patients with PEW have clinical and biochemical evidence of malnutrition and inflammation and the condition is associated with poorer mental functions.
Probing the active site of homoserine trans‐succinylase (2004)

Homoserine trans-succinylase is the first enzyme in methionine biosynthesis of Escherichia coli and catalyzes the activation of homoserine via a succinylation reaction. The in vivo activity of this enzyme is subject to tight regulation by several mechanisms, including repression and activation of gene expression, feedback inhibition, temperature regulation and proteolysis. This complex regulation reflects the key role of this enzyme in bacterial metabolism. Here, we demonstrate--using proteomics and high-resolution mass spectrometry--that succinyl is covalently bound to one of the two adjacent lysine residues at positions 45 and 46. Replacing these lysine residues by alanine abolished the enzymatic activity. These findings position the lysine residues, one of which is conserved, at the active site.
Configuration Interaction of Hydropathic Waves Enables Ubiquitin Functionality (2016)

Ubiquitin, discovered less than 50 years ago, tags thousands of diseased proteins for destruction. It is small (only 76 amino acids), and is found unchanged in mammals, birds, fish and even worms. Key features of its functionality are identified here using critical point thermodynamic scaling theory. These include Fano interference between first- and second-order elements of globular surface shape transitions. Comparison with its closest relative, 76 amino acid Nedd8, shows that the latter lacks these features. A cracked elastic network model is proposed for the common target shared by many diseased proteins.
Combined Deficiency in Glutathione Peroxidase 4 and Vitamin E Causes Multiorgan Thrombus Formation and Early Death in Mice (2013)

Here, we show for the first time that in the absence of Gpx4, sufficient vitamin E supplementation is crucial for endothelial viability.
Optimal Aggregation of RF and VLC Bands for Beyond 5G Mobile Services (2022)

The integration of Radio Frequency (RF) and Visible Light Communication (VLC) technologies has been considered an enabler to achieving the Key Performance Indicators (KPIs) in Beyond 5G (B5G). Apart from higher data rates for enhanced Mobile Broadband applications, Ultra-Reliable and Low-Latency Communications and massive Machine-Type Communications must be also supported. This poses notable challenges in the design of a mobile communication system that relies exclusively on the use of licensed RF spectrum. In order to cope with the requirements of B5G services, the complementary benefits that RF and VLC bands have in terms of communication bandwidth, signal propagation characteristics, and ultra-densification feasibility, can be exploited. For this purpose, this paper studies the performance of two integration approaches, namely RF - VLC selection (Layer-3 or network-layer) and RF-VLC aggregation (Layer-2 or MAC-layer). Based on the obtained simulation results, it is possible to conclude that RF - VLC aggregation outperforms RF - VLC selection in terms of data rate performance, especially when ultra-reliable communication services are required to connect a large number of user terminals placed in an indoor scenario.
Assigning clinical meaning to somatic and germline whole exome sequencing data to guide cancer precision medicine. (2016)

11565 Background: Implementing cancer precision medicine requires interpretation of each potentially clinically relevant and biologically meaningful genomic alteration to aid clinical decision-making. We developed a systematic approach to this challenge through the CanSeq program, a prospective study of tumor and germline whole exome sequencing (WES) in patients with metastatic colorectal and lung cancer. Methods: WES was performed on DNA extracted from FFPE tumor biopsies and matched blood samples from 242 patients. Data were analyzed to identify point mutations, indels, and copy number alterations. Variants were ranked according to therapeutic and biological relevance using PHIAL, an analytical software tool. Levels of evidence were assigned to clinical implications associated with each variant. Decisions to return results to participants were initially made by a molecular tumor board, and ultimately evolved to a guideline-based interpretive algorithm to allow scalability. Results: 165/242 participants have had WES analyzed, interpreted, and returned to their clinical team. Of 768 somatic variants evaluated, 511 (67%) were determined to be potentially clinically relevant and reported to clinical teams. Of these, 31% classified as having clinical evidence, 21% pre-clinical evidence, and 48% theoretical/inferential rationales. Among 806 curated germline variants, only 5% were deemed clinically relevant and reported to clinical teams. Among returned germline variants, 47% were classified as pathogenic, 16% as likely pathogenic, and 37% as variants of uncertain significance in a gene related to the patient’s cancer. In total, 91% of patients had an actionable or potentially actionable somatic alteration; 21% had at least one reported germline alteration. Conclusions: This systematic interpretive framework effectively identifies clinically relevant somatic and germline alterations. There was a significant difference in the proportion of reported somatic and germline alterations. Although the majority of cases harbored at least one potentially clinically relevant somatic alteration, we observed wide variations in the strength of evidence associated with these alterations.
Quantum numbers of the X(3872) state and orbital angular momentum in its p[superscript 0]J/ψ decay (2015)

Angular correlations in B[superscript +] → X(3872)K[superscript +] decays, with X(3872) → ρ[superscript 0]J/ψ, ρ[superscript 0] → π[superscript +]π[superscript -] and J/ψ → μ[superscript +]μ[superscript -], are used to measure orbital angular momentum contributions and to determine the J[superscript PC] value of the X(3872) meson. The data correspond to an integrated luminosity of 3.0 fb[superscript -1] of proton-proton collisions collected with the LHCb detector. This determination, for the first time performed without assuming a value for the orbital angular momentum, confirms the quantum numbers to be J[superscript PC] = 1[superscript ++]. The X(3872) is found to decay predominantly through an S wave and an upper limit of 4% at 95% C.L. is set on the D-wave contribution.
Effect of passive immunization on immunogenicity and protective efficacy of vaccination against a Mexican low‐pathogenic avian H5N2 influenza virus (2013)

Vaccine efficacy against LP H5N2 in Mexico can be severely reduced by maternal antibodies. Source-dependent antisera effects offer the possibility of further elucidation of the immunosuppressive components involved.
Impact of the Major Candida glabrata Triazole Resistance Determinants on the Activity of the Novel Investigational Tetrazoles VT-1598 and VT-1161 (2019)

VT-1161 and VT-1598 are promising investigational tetrazole antifungals that have shown <i>in vitro</i> and <i>in vivo</i> activity against <i>Candida</i> and other fungi. <i>Candida glabrata</i> is a problematic opportunistic pathogen that is associated with high mortality in invasive infection, as well as both intrinsic and rapidly acquired antifungal resistance. The MICs of VT-1161 and VT-1598 were determined by CLSI methodology to evaluate their <i>in vitro</i> activities against clinical <i>C. glabrata</i> isolates and strains containing individual deletions of the zinc cluster transcription factor genes <i>PDR1</i> and <i>UPC2A</i> as well as the efflux transporter genes <i>CDR1</i>, <i>PDH1</i>, and <i>SNQ2</i> Overall, both tetrazoles demonstrated relative activities comparable to those of the tested triazole antifungals against clinical <i>C. glabrata</i> isolates (MIC range, 0.25 to 2 mg/liter and 0.5 to 2 μg/ml for VT-1161 and VT-1598, respectively). Deletion of the <i>PDR1</i> gene in fluconazole-resistant matched clinical isolate SM3 abolished the decreased susceptibility phenotype completely for both VT-1161 and VT-1598, similarly to the triazoles. <i>UPC2A</i> deletion also increased susceptibility to both triazoles and tetrazoles but to a lesser extent than <i>PDR1</i> deletion. Of the three major transporter genes regulated by Pdr1, <i>CDR1</i> deletion resulted in the largest MIC reductions for all agents tested, while <i>PDH1</i> and <i>SNQ2</i> deletion individually impacted MICs very little. Overall, both VT-1161 and VT-1598 have comparable activities to those of the available triazoles, and decreased susceptibility to these tetrazoles in <i>C. glabrata</i> is driven by many of the same known resistance mechanisms.
Representativeness and Weighting Methods of Real Time Accident Data in India (2013)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The 2011 Report of Ministry of Road Transport and Highways, Government of India states that the total accidents with injuries is estimated about 497, 686 out of which the injuries are 511, 394 and fatalities are 142, 485, an average of one fatality per 3.5 [&lt;span class="xref"&gt;1&lt;/span&gt;]. Social losses on account of these crashes are estimated at over Rupees 100 000 Crores annually or 3% of our Gross Domestic Product (GDP) [&lt;span class="xref"&gt;2&lt;/span&gt;]. The irony is that these causalities are rising at 5.9 % annually. India accounts for 10% of the global road crash fatalities. Therefore traffic safety became very important in India. In order to understand the root causes of accidents data is needed in more detail which could be analyzed and points out the major issues to find solutions to stop this trend. Besides vehicle safety, infrastructure related issues and education skills can be derived out of accident data.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Official statistics regarding accidents in India are available in national and state wise reports. More detailed information about accident causes, accident conditions and consequences are roughly obtained. There is a lack of engineering data in the available reports. To address traffic safety related issues like infrastructure, driving behaviour and benefit of vehicle safety systems more detailed accident data is needed.&lt;/div&gt;&lt;/div&gt;
Formation of visual memories controlled by gamma power phase-locked to alpha oscillations (2016)

Neuronal oscillations provide a window for understanding the brain dynamics that organize the flow of information from sensory to memory areas. While it has been suggested that gamma power reflects feedforward processing and alpha oscillations feedback control, it remains unknown how these oscillations dynamically interact. Magnetoencephalography (MEG) data was acquired from healthy subjects who were cued to either remember or not remember presented pictures. Our analysis revealed that in anticipation of a picture to be remembered, alpha power decreased while the cross-frequency coupling between gamma power and alpha phase increased. A measure of directionality between alpha phase and gamma power predicted individual ability to encode memory: stronger control of alpha phase over gamma power was associated with better memory. These findings demonstrate that encoding of visual information is reflected by a state determined by the interaction between alpha and gamma activity.
Linear modeling of modern artist paints using a modification of the opaque form of Kubelka‐Munk turbid media theory (2016)

Abstract A new model of turbid medium theory is proposed that combines the best parts of the opaque forms of Kubelka‐Munk single and two constant models. This model introduces an impurity index, a spectrally nonselective scattering coefficient for each chromatic component. The new model is shown to have a convex, linear dependence on colorant concentration so that it can be used for colorant identification in high‐resolution images of works of art while offering an extension to the single constant model that can predict the absorption and scattering of paints, both in mixture and pure (masstone) forms. The model was tested and validated using 28 matte acrylic dispersion paints, of the type used in modern painting. These paints had a wide range of absorption and scattering characteristics. © 2016 Wiley Periodicals, Inc. Col Res Appl, 42, 308–315, 2017
On the coverage problem in video-based wireless sensor networks (2005)

Video-based wireless sensor networks continue to gain increasing interest due to their ability to collect visual information for a wide range of applications. However, knowledge about these types of networks is mostly related to visual algorithms, leaving the networking perspective aside. In this work, we analyze how an algorithm designed for traditional wireless sensor networks, which integrates the coverage and routing problem, behaves in video-based networks. Our results show that because of the unique way that cameras capture data, the sensor network algorithm does not give the expected results in terms of coverage preservation of monitored areas. We discuss the main differences between traditional wireless sensor networks and video-based networks that lead to such a result, and we provide ideas for how protocols should be designed for the unique features of video-based networks
Fault isolation in parallel coupled wind turbine converters (2010)

Parallel converters in wind turbine give a number advantages, such as fault tolerance due to the redundant converters. However, it might be difficult to isolate gain faults in one of the converters if only a combined power measurement is available. In this paper a scheme using orthogonal power references to the converters is proposed. Simulations on a wind turbine with 5 parallel converters should a clear potential of this scheme for isolation of this gain fault to the correct converter in which the fault occurs.
The Effect of Processing Additives on Energetic Disorder in Highly Efficient Organic Photovoltaics: A Case Study on PBDTTT‐C‐T:PC71BM (2015)

Energetic disorder, an important parameter affecting the performance of organic photovoltaics, is significantly decreased upon the addition of processing additives in a highly efficient benzodithiophene-based copolymer blend (PBDTTT-C-T:PC71 BM). Wide-angle and small-angle X-ray scattering measurements suggest that the origin of this reduced energetic disorder is due to increased aggregation and a larger average fullerene domain size together with purer phases.