gebhart/patrepeval huggingface dataset:
The Detection of Starvation-specific Antigens in Two Marine Bacteria (1987)

SUMMARY: Antisera produced against starved cells of two marine bacteria (a Vibrio sp. and an unidentified Gram-negative motile rod) were titrated in order to quantify with respect to time of starvation the appearance of starvation-specific antigens. Polyacrylamide gels of lipopolysaccharide digests, and of total protein and membrane and periplasmic fractions, were prepared, blotted and immunoassayed to determine the location(s) of the antigenic response. For the Vibrio isolate, no starvation-specific antigens were detected, but such antigens were detected for the other isolate; they were proteinaceous and were located in the outer membrane and periplasmic space. Titrations of whole cells indicated that the antigenic change in the cell surface occurred in the initial phase of starvation and increased during the first 14 h of the starvation period studied.
Evaluation of the dedicated breast PET imaging technique including axillary region (2021)

3020 Introduction: Metabolic imaging of the primary breast tumor with 18F-fluorodeoxyglucose (FDG) PET may assist in predicting treatment response. Dedicated breast PET (dbPET) systems are expected to detect small breast cancers than conventional whole-body PET by targeting only one breast at a time and imaging the breast close to a small aperture, thereby enabling local imaging with high spatial resolution. On the other hand, there is a problem that blind areas may exist in areas close to the chest wall or the axillary region due to its small aperture. However, additional imaging of the axillary region may help overcome this problem. In this study, we evaluated a technique for imaging the breast and axillary region using a ring-shaped dbPET system. Materials and Methods: Ten preoperative cases of breast cancer in which FDG PET scans were performed between October and December 2020 were included in the study. After 90 minutes of FDG administration, breast scan was performed with dbPET system (SET-5002, Shimadzu) in a prone position. And the axillary regions were scanned with the arm plunged shoulder-deep into the PET detector. The acquisition time was set at 5 minutes for each region. Fused images were created by the dbPET data and the previously obtained contrast-enhanced MRI images. And the blind area of mammary region in dbPET data was evaluated per mammary gland area. Results: 
In the case of breast scans only, the incidence of blind areas were 10%, 30%, 30%, 20%, and 100% in the Upper Outer Quadrant, Lower Inner Quadrant, Upper Outer Quadrant, Lower Outer Quadrant, and axillary regions, respectively. And, the incidence was reduced to 10%, 30%, 10%, 0%, and 10% when additional axillary scan was performed. Conclusions: In this study, we evaluated a new imaging technique using a ring-shaped dbPET system. These data indicated that additional imaging of the axillary region might be synergic and complementary for more accurate dbPET examination.
Solution NMR structure of the 30S ribosomal protein S28E from <i>Pyrococcus horikoshii</i> (2003)

Abstract We report NMR assignments and solution structure of the 71‐residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii , target JR19 of the Northeast Structural Genomics Consortium. The structure, determined rapidly with the aid of automated backbone resonance assignment (AutoAssign) and automated structure determination (AutoStructure) software, is characterized by a four‐stranded β‐sheet with a classic Greek‐key topology and an oligonucleotide/oligosaccharide β‐barrel (OB) fold. The electrostatic surface of S28E exhibits positive and negative patches on opposite sides, the former constituting a putative binding site for RNA. The 13 C‐terminal residues of the protein contain a consensus sequence motif constituting the signature of the S28E protein family. Surprisingly, this C‐terminal segment is unstructured in solution.
AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data (2021)

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.
Transforming MOFs for Energy Applications Using the Guest@MOF Concept (2016)

As the world transitions from fossil fuels to clean energy sources in the coming decades, many technological challenges will require chemists and material scientists to develop new materials for applications related to energy conversion, storage, and efficiency. Because of their unprecedented adaptability, metal-organic frameworks (MOFs) will factor strongly in this portfolio. By utilizing the broad synthetic toolkit provided by the fields of organic and inorganic chemistry, MOF pores can be customized to suit a particular application. Of particular importance is the ability to tune the strength of the interaction between the MOF pores and guest molecules. By cleverly controlling these MOF-guest interactions, the chemist may impart new function into the Guest@MOF materials otherwise lacking in vacant MOF. Herein, we highlight the concept of the Guest@MOF as it relates to our efforts to develop these materials for energy-related applicatons. Our work in the areas of H2 and noble gas storage, hydrogenolysis of biomass, light-harvesting, and conductive materials will be discussed. Of relevance to light-harvesting applications, we report for the first time a postsynthetic modification strategy for increasing the loading of a light-sensitive electron-donor molecule in the pores of a functionalized MIL-101 structure. Through the demonstrated versatility of these approaches, we show that, by treating guest molecules as integral design elements for new MOF constructs, MOF science can have a significant impact on the advancement of clean energy technologies.
Patterns of Laser Activation During Ureteroscopic Lithotripsy: Effects on Caliceal Fluid Temperature and Thermal Dose (2021)

<b><i>Introduction:</i></b> Characterizing patterns of laser activation is important for assessing thermal dose during laser lithotripsy. The objective of this study was twofold: first, to quantify the range of operator duty cycle (ODC) and pedal activation time during clinical laser lithotripsy procedures, and second, to determine thermal dose in an <i>in vitro</i> caliceal model when 1200 J of energy was applied with different patterns of 50% ODC for 60 seconds. <b><i>Methods:</i></b> Data from laser logs of ureteroscopy cases performed over a 3-month period were used to calculate ODC (lasing time/lithotripsy time). Temporal and rolling 1-minute average power tracings were generated for each case. <i>In vitro</i> experiments were conducted using a 21 mm diameter glass bulb in a 37°C water bath, simulating a renal calix. A LithoVue ureteroscope with attached thermocouple was inserted and 8 mL/min irrigation was delivered with a 242 μm laser fiber within the working channel. In total, 1200 J of laser energy was applied in five different patterns at 20 W average power for 60 seconds. Thermal dose was calculated using the Sapareto and Dewey <i>t</i><sub>43</sub> method. <b><i>Results:</i></b> A total of 63 clinical cases were included in the analysis. Mean ODC was 32% overall and 63% during the 1-minute of greatest energy delivery. Mean time of pedal activation was 3.6 seconds. <i>In vitro</i> studies revealed longer pedal activation times produced higher peak temperature and thermal dose. Thermal injury threshold was reached in 9 seconds when 40 W was applied at 50% ODC with laser activation patterns of 30 seconds on/off and 15 seconds on/off. <b><i>Conclusion:</i></b> ODC was quantified from clinical laser lithotripsy cases: 32% overall and 63% during 1-minute of peak power. Time of pedal activation is an important factor contributing to fluid heating and thermal dose. Awareness of these concepts is necessary to reduce risk of thermal injury during laser lithotripsy procedures.
TWIN as a future-proof optical transport technology for next generation metro networks (2016)

The continuous growth of the traffic at a rapid pace raises challenges related to the efficient use of resources and saving of energy in the transport network. The new traffic pattern is characterized by faster growth of metro traffic compared with core, due in part to video content replication. In this paper, we compare the resource requirements of three different transport technologies (optical packet switching, opaque circuit switching and transparent circuit switching) within two architecture scenarios (the current hub-and-spoke architecture and the next generation distributed architecture). The comparison study takes into consideration the predicted traffic growth from 2014 to 2019 and the potential traffic decentralization due to content replication. For the optical packet switching, we focus on Time-domain Wavelength Interleaved Network (TWIN) solution which achieves passive switching at the intermediate nodes thanks to the precomputed optical packet emission schedule. Results show that TWIN outperforms the other transport technologies in terms of number of transmitters and receivers with a high ability to cope with scalability issues.
Automatic Prediction of Facial Trait Judgments: Appearance vs. Structural Models (2011)

Evaluating other individuals with respect to personality characteristics plays a crucial role in human relations and it is the focus of attention for research in diverse fields such as psychology and interactive computer systems. In psychology, face perception has been recognized as a key component of this evaluation system. Multiple studies suggest that observers use face information to infer personality characteristics. Interactive computer systems are trying to take advantage of these findings and apply them to increase the natural aspect of interaction and to improve the performance of interactive computer systems. Here, we experimentally test whether the automatic prediction of facial trait judgments (e.g. dominance) can be made by using the full appearance information of the face and whether a reduced representation of its structure is sufficient. We evaluate two separate approaches: a holistic representation model using the facial appearance information and a structural model constructed from the relations among facial salient points. State of the art machine learning methods are applied to a) derive a facial trait judgment model from training data and b) predict a facial trait value for any face. Furthermore, we address the issue of whether there are specific structural relations among facial points that predict perception of facial traits. Experimental results over a set of labeled data (9 different trait evaluations) and classification rules (4 rules) suggest that a) prediction of perception of facial traits is learnable by both holistic and structural approaches; b) the most reliable prediction of facial trait judgments is obtained by certain type of holistic descriptions of the face appearance; and c) for some traits such as attractiveness and extroversion, there are relationships between specific structural features and social perceptions.
Bidirectional 4-PAM to Double Per-Fiber Capacity in 2-km Intra-Datacenter Links (2018)

This paper presents an experimental demonstration of bidirectional 4-PAM transmission for intra-datacenter links using a pair of SMF fibers. In the proposed architecture, each transceiver laser feeds both fibers, which are thus used bidirectionally to double the capacity per used fiber, wavelength, and laser. Besides the experimental demonstration, we also report a theoretical and simulative investigation on the penalty induced in this architecture by spurious connector back-reflections. We show that the resulting penalty can be kept under control for typical realistic connector reflection values, provided that each pair of lasers in both directions are separated by at least twice the system symbol rate.
on-State Performance Enhancement and Channel-Direction-Dependent Performance of a Biaxial Compressive Strained $ \hbox{Si}_{0.5}\hbox{Ge}_{0.5}$ Quantum-Well pMOSFET Along $ \langle \hbox{110} \rangle$ and $\langle \hbox{100} \rangle$ Channel Directions (2011)

pMOSFET performance of high Ge content (~50%) biaxial compressive strained SiGe heterostructure channel pMOSFETs is characterized, and performance between 〈110 〉 and 〈100 〉 channel orientations on a (001) substrate is compared for physical channel lengths down to ~80 nm. Temperature-dependent mobility and velocity are characterized for both channel directions. First, it is shown that high Ge content SiGe-based channels can deliver drive current enhancement over unstrained Si below sub-100-nm channel lengths. Second, it is found that, with a higher Ge content SiGe channel under biaxial compressive strain, there is a difference of drive current between 〈110 〉 and 〈100 〉 channel directions, and the difference increases when temperature is lowered and/or when channel length is scaled down. An external series resistance difference is detected between two channel directions, although it appears to be insufficient to explain all the direction-dependent drive current difference. Channel transport behavior in different channel orientations can be clearly observed with low external source/drain (S/D) series resistance achieved with a millisecond S/D dopant activation anneal process while controlling the thermal budget. Two possibilities have been investigated to understand channel-direction-dependent performance: possible differences in effects of device processing impact between two channel directions and anisotropic transport effects from an anisotropic hole band structure, particularly under biaxial compressive strain in a SiGe channel pseudomorphically grown on a Si substrate.
Antibody constructs for radioimmunodiagnosis and treatment of human pancreatic cancer (2000)

Pancreatic cancer (PC) is a common disease that is seldom cured. Current approaches to the treatment of PC are not effective because the non-specific nature of both chemotherapy and external beam radiation results in toxicity to normal tissue. Monoclonal antibodies (MAbs) can be used as selective carriers for delivering radionuclides, toxins, or cytotoxic drugs to malignant cell populations. Therefore, MAb-technology has led to a significant amount of research in targeted therapy. Targeted therapy would generally allow the concentration of cytotoxic agents in tumors and would markedly lessen the toxicity to normal tissues, which limits the dosage and effectiveness of systemically administered drugs. A variety of MAbs are being pre-clinically evaluated for the diagnosis and treatment of PC. Novel recombinant antibody constructs hold a promising future in both the diagnosis and treatment of cancer. By genetic-engineering methods, several high affinity antibody fragments with optimum tumor targeting properties, such as higher functional affinity (divalent and multivalent scFvs) and blood residence time (good tumor localization with high radiolocalization index), have been generated. Animal models have permitted the in vivo assessment of these antibody-based reagents, therapeutic/diagnostic radionuclide, radiolabeling conditions, and efficacy of administration regimes. For PC, immunoscintigraphy using MAbs has taken new strides. The use of MAbs and their fragments for radioimmunoguided surgery and therapy of PC has shown encouraging results at preclinical levels and warrants further attention.
Mast cell heterogeneity and hyperplasia in bleomycin-induced pulmonary fibrosis of rats. (1984)

The distribution, density, and histochemical subtype of mast cells were studied in the respiratory tract of rats with bleomycin-induced pulmonary fibrosis. In normal rats, mast cell densities were highest in the trachea and lowest in the bronchus and parenchyma. Two histochemically distinct mast cell populations were identified in the mucosa adjacent to the tracheal cartilage, but elsewhere only a single population of typical connective tissuelike mast cells was found. After intratracheally administered bleomycin, lung histamine levels (micrograms/g wet weight) increased as much as 14-fold by Day 50. Pulmonary mast cell changes were present early in the fibrotic process, and by Day 14 the mast cell density in the parenchyma was 10 times normal. These parenchymal mast cells were histochemically of the connective tissue type. Thus, pronounced mast cell hyperplasia occurs during the evolution of experimental pulmonary fibrosis. This model provides a powerful tool to study pulmonary mast cells and to identify their role in fibrotic disease.
Safety evaluation of the food enzyme preparation isomaltulose synthase from Serratia plymuthica strain Z12A (2021)

The food enzyme isomaltulose synthase (sucrose glucosylmutase; EC 5.4.99.11) is produced with <i>Serratia plymuthica</i> strain Z12A by BENEO-Palatinit GmbH. The food enzyme is used only in the form of an immobilised preparation of non-viable cells for the production of isomaltulose. Residual amounts of total organic solids (TOS) are removed by the purification steps applied during the production of isomaltulose consequently, dietary exposure was not calculated. Genotoxicity tests did not indicate safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level of 1,011 mg TOS/kg body weight (bw) per day, the highest dose tested. Similarity of the amino acid sequence of the enzyme to those of known allergens was searched and no match was found. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions by dietary exposure cannot be excluded, but the likelihood of such reactions to occur is considered to be low. Based on the data provided, the use of an immobilised food enzyme and the removal of TOS during the production of isomaltulose the Panel concluded that this food enzyme preparation does not give rise to safety concerns under the intended conditions of use.
NK-cell education is shaped by donor HLA genotype after unrelated allogeneic hematopoietic stem cell transplantation (2010)

The rules governing natural killer (NK)-cell education in the allogeneic environment created by unrelated hematopoietic stem-cell transplantation (HSCT) are still largely elusive, especially in an unrelated donor setting. NK-cell inhibitory receptors for self-human leukocyte antigen (HLA) play a central role in the acquisition or maintenance of NK-cell functional competence. Therefore, the responsiveness of different NK-cell subsets was assessed as a function of their expression or absence of expression of self-HLA-specific inhibitory receptors, in a large cohort (n = 60) of unrelated HSCT recipients. A fully effective NK-cell education process was achieved within the first year after allogeneic HSCT and lasted for at least 3 years thereafter. In addition, HLA-mismatched HSCT led to a stable education pattern that was determined by the donor's HLA ligands. These data suggest that the NK cell's education partner could be of hematopoietic rather than extrahematopoietic origin. This donor-ligand-driven NK-cell education model would suggest a sustained graft-versus-leukemia effect after HLA-mismatched HSCT.
A measurement-based distributed large-signal E/O circuit model for high-speed electroabsorption modulators (2004)

The paper presents a measurement-based largesignal distributed model for high-speed electroabsorption modulators, integrated within an RF circuit CAD environment. The model is implemented through a cascaded-cell approach; the identification of the nonlinear lumped equivalent circuit parameters of each cell through measurements is discussed and an example is provided of circuit extraction. An example of integrated driver-EAM simulation is finally discussed.
Mechanisms of myocardial hypercarbic acidosis during cardiac arrest (1995)

During the global myocardial ischemia of cardiac arrest and during regional myocardial ischemia due to local impairment of coronary blood flow, intramyocardial carbon dioxide tensions (Pmco2) of ischemic myocardium increase to levels exceeding 400 Torr. The mechanism of such myocardial hypercarbic acidosis is as yet incompletely understood, specifically whether these increases in Pmco2 are due to increased oxidative metabolism, decreased CO2 removal, or buffering of metabolic acids. We therefore measured Pmco2 and the total CO2 content of rat hearts harvested before, during, and after resuscitation from cardiac arrest. Pmco2 significantly increased from an average of 63 to 209 Torr during a 4-min interval of untreated ventricular fibrillation. This was associated with concurrent decreases in intracellular pH from an average of 7.03 to 6.02 units. The total CO2 content of the myocardium simultaneously decreased from 17.0 to 16.5 mmol/kg. Accordingly, increases in Pmco2 and [H+] were observed in the absence of increases in the total CO2 content and therefore the calculated myocardial bicarbonate. These observations in the rat model implicate buffering of metabolic acids by bicarbonate rather than increases in CO2 production or decreases in CO2 removal as the predominant mechanism accounting for myocardial hypercarbia.
A Framework to Evaluate the Economic Impact of Pharmacogenomics (2006)

A general tool for predicting the impact of pharmacogenomic-based diagnostic tests on healthcare costs in asthma patients suggests that upfront testing costs are likely offset by avoided nonresponse costs. We suggest that similar analyses for decision making could be undertaken using claims data in which a population can be stratified by response to a drug.
Percutaneous Balloon Valvuloplasty and Mitral Valve Repair (2009)

Percutaneous therapies for valvular heart disease were employed as early as the 1950s, using a wire valvulotome to treat pulmonic stenosis. The contemporary era of catheter therapy for valve lesions began with the introduction of balloon mitral valvotomy by Inoue in 1982. Descriptions of balloon aortic valvuloplasty (BAV) and balloon mitral valvotomy (BMV) using a variety of techniques followed over the ensuing decade. During that time and until recently, treatment for regurgitant lesions and the potential to replace valves percutaneously were distant concepts. Balloon valvotomy has matured and reached its plateau, while new mitral valve repair therapies for mitral regurgitation (MR) and aortic valve replacement approaches are developing rapidly. This chapter will review in detail the techniques of BAV and BMV. In addition there will be a detailed discussion of percutaneous mitral valve repair technologies and approaches. Despite the limitations of balloon therapy for stenotic lesions, there are still well-defined roles for both BMV and BAV. BMV is the preferred therapy for most patients with mitral stenosis, while BAV is an effective palliative therapy in highly selected high-risk patients with aortic valve stenosis.