gebhart/patrepeval huggingface dataset:
Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation (2017)

The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this study will support the ongoing research for this particular animal model and provides a new molecular tool to assist biological research in cartilaginous fishes.
Excitation of LP 21b and LP 02 modes with PLC-based tapered waveguide for mode-division multiplexing (2016)

Multi-stage mode conversion technique, using asymmetric directional couplers and tapered mode converters, for launching LP 21b and LP 02 mode on PLC for six mode multi/demultiplexer is proposed. Successful excitation of these modes are demonstrated.
Compensation of distant phase-distorting layers I Narrow-field-of-view adaptive receiver system (2004)

We analyze various scenarios of adaptive wave-front phase-aberration correction in optical-receiver-type systems when inhomogeneties of the wave propagation medium are either distributed along the propagation path or localized in a few thin layers remotely located from the receiver telescope pupil. Phase-aberration compensation is performed with closed-loop control architectures based on decoupled stochastic parallel gradient descent, stochastic parallel gradient descent, and phase conjugation control algorithms. Both receiver system aperture diffraction effects and the effect of wave-front corrector position on phase-aberration compensation efficiency are analyzed.
Device for Safely Closing Trocar Sites in Minimally Invasive Abdominal Surgery (2017)

Laparoscopic and robotic surgeries of the abdomen require a trocar to facilitate entry and removal of instrumentation. Some of these trocars are 5mm or less, but some trocars for these surgeries are larger, with 8mm to 15mm trocars commonly used. One of the well-known problems seen in minimally invasive surgery to the abdomen is the resulting defect left in the abdominal wall following removal of the trocars. Occasionally, especially after removal of larger trocars, a defect is left that is large enough to allow omentum or segments of small intestine to become entrapped within the resulting space in the abdominal wall. These trocar site hernias can cause pain, but they also may lead to small bowel obstruction and bowel ischemia or even infarction, perforation and death. The likelihood of a trocar site hernia is increased when the minimally invasive procedure requires removal of an organ or a mass. This often requires dilatation of the trocar site opening.1,2,3 Re-operation to reduce and repair trocar site hernias adds significant cost to the healthcare system. Two separate studies report that incidence of trocar site hernias are in the ranges of 0.65%–2.8%4 and 1.5%–1.8%5,6. Based on a 2016 report published by the American Society for Metabolic and Bariatric Surgery (ASMBS), 196,0007 bariatric procedures were performed in 2015. Assuming an average incidence rate of 1.7%, and based on the cost analysis provided by a 2008 case study8, in bariatric surgery alone, it is estimated that the treatment and hospitalization of such hernias adds an additional $86.2M to healthcare costs. Several methods and devices exist to prevent the occurrence of trocar site hernias. However, closing superficial fascia externally is difficult, especially in obese patients, and often requires extending the skin incision significantly. Most instruments to close the potential hernia site involve introducing a hollow needle with a built-in, grasping device through tissue on one side of the defect and into the abdominal cavity. This puts internal structures at risk for potential injury. One end of suture is introduced with this needle and then using a separate instrument through a different trocar this suture is held while the needle is removed. The needle device is then re-introduced through tissue on the opposite side of the defect, and the suture is handed back to the needle device and pulled out completing a U-stitch to close the potential hernia site. If a surgeon inserts a finger into the abdomen along the trocar site to guide the needle, there is the potential for injury to the surgeon’s finger. Therefore, we set about to design a device to close trocar site defects that would work efficiently, while being safe from injury to the patient or the surgeon, and preferably without the need for a separate instrument through a different trocar to assist.
One‐Pot Synthesis of Functional Helicoidal Hybrid Organic–Inorganic Nanofibers with Periodically Organized Mesoporosity (2009)

Abstract The one‐pot synthesis and properties of multifunctional hybrid mesoporous organosilica fibers with helical shapes are described. These hybrid mesoporous fibers are prepared without chiral elements and functionalized with a large variety of organic R functions (R = alkylthiols, phenylsulfonates, alkylphosphonates, dansyl, aminopropyl, fluoroalkyl, etc.). The resulting nanomaterials are thoroughly characterized by a variety of techniques. The use of a synergetic combination of achiral molecules as co‐directing structuring agents, a surfactant, and an organofunctional silica precursor R‐Si(OR) 3 allows, via carefully tuning of the main synthesis parameters and processing conditions, to control the shape, which is the anisotropic factor, of the hybrid nanofibers. The functionalization of the hybrid materials with fluorescent molecules (dansyl) and gold nanoparticles opens possibilities for sensor and catalytic applications, respectively. Moreover, these hybrid nanofibers can be easily transferred in organic solvents or in a “green” solvent such as water to make stable colloidal dispersions. This tunable functionality of nanofibers also allows their transferability into a variety of polymeric hosts (PVDF, PVBu, and PVP) allowing the formation of functional homogeneous nanocomposite hybrid membranes.
The interaction of Cl(2P3/2) and Cl(2P1/2) with n-Si(100): Spontaneous etching (1991)

The sticking coefficient γ of ground-state Cl (Cl 2P3/2 ) and spin–orbit excited Cl* (Cl 2P1/2 ) on lightly doped n-Si(100) was measured using resonance-enhanced multiphoton ionization of Cl and Cl* at mTorr pressure in a Knudsen cell. For Cl only an upper limit of γ≤5×10−5 could be obtained and for Cl* γ=4.6×10−4 was measured. These γ values are temperature independent in the range of 300–600 K and the sum corresponds to a spontaneous etch rate of 9.4 Å/min for Si(100). SiCl2 was the principal etch product under these spontaneous etch conditions, and no SiCl4 was found over the given temperature range.
Application of 300× Enhanced Fluorescence on a Plasmonic Chip Modified with a Bispecific Antibody to a Sensitive Immunosensor (2013)

The grating substrate covered with a metal layer, a plasmonic chip, and a bispecific antibody can play a key role in the sensitive detection of a marker protein with an immunosensor, because of the provision of an enhanced fluorescence signal and the preparation of a sensor surface densely modified with capture antibody, respectively. In this study, one of the tumor markers, a soluble epidermal growth factor receptor (sEGFR), was selected as the target to be detected. The ZnO- and silver-coated plasmonic chip with precise regularity and the appropriate duty ratio in the periodic structure further enhanced the fluorescence intensity. As for sensor surface modification with capture antibody, a bispecific antibody (anti-sEGFR and anti-ZnO antibody), the concentrated bispecific antibody solution was found to nonlinearly form a surface densely immobilized with antibody, because the binding process of a bispecific antibody to the ZnO surface can be a competitive process with adsorption of phosphate. As a result, the interface on the plasmonic chip provided a 300× enhanced fluorescence signal compared with that on a ZnO-coated glass slide, and therefore sEGFR was found to be quantitatively detected in a wide concentration range from 10 nM to 700 fM on our plasmonic surface.
Abstract IA25: Systematic interrogation of KRAS function (2023)

Abstract Oncogenic mutations of KRAS occur frequently in pancreas, lung and colon cancers. Recent efforts to target particular KRAS alleles or RAS effector pathways has led to clinical responses but resistance to therapy limits the effectiveness of these therapies. To understand the role of KRAS in tumor initiation and maintenance, we have used systematic approaches to understand dependencies in KRAS-driven cancers. Specifically, we have used genome scale gain and loss of function screens to interrogate pathways necessary for the survival of KRAS-driven cancers. We have identified genes that required for the survival of KRAS-driven cancers and that canonical RAS signaling proteins have multiple functions. Together these on-going approaches provide new insights into KRAS signaling and identify potential targets for combination therapies for KRAS driven cancers. Citation Format: William C. Hahn. Systematic interrogation of KRAS function [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr IA25.
Mechanical Response of Rat Cortical Neurons: AFM Indentations and Preliminary Modeling (2009)

Traumatic brain injury (TBI) due to blast exposure is becoming increasingly prevalent in soldiers returning from war and some consider TBI to be the signature wound of the Iraq and Afghanistan conflicts [1]. Common causes are exposure to explosions of improvised explosive devices (IEDs), rocket-propelled grenades, and landmines. A study by Hoge et al found that of 2525 soldiers, 4.9% reported injuries with loss of consciousness and an additional 10.3% reported injuries with altered mental status [2]. Despite the prevalence of TBI, little is known on the epidemiology of mild TBI and on its long-term health consequences. An improved understanding of the damage mechanism and injury progression will be critical for designing better protective gear and selecting appropriate treatments.
Oxidative N-dearylation of 2-azetidinones. p-Anisidine as a source of azetidinone nitrogen (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxidative N-dearylation of 2-azetidinones. p-Anisidine as a source of azetidinone nitrogenDavid R. Kronenthal, C. Y. Han, and Martha K. TaylorCite this: J. Org. Chem. 1982, 47, 14, 2765–2768Publication Date (Print):July 1, 1982Publication History Published online1 May 2002Published inissue 1 July 1982https://pubs.acs.org/doi/10.1021/jo00135a016https://doi.org/10.1021/jo00135a016research-articleACS PublicationsRequest reuse permissionsArticle Views2131Altmetric-Citations224LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Continuous speech recognition in the WAXHOLM dialogue system (2007)

This paper presents the status of the continuous speech recognition engine of the WAXHOLM project. The engine is a software only system written in portable C code. The design is flexible and different modes for phonetic pattern matching are available. In particular, artificial neural networks and standard multiple Gaussian mixtures are implemented for phone probability estimation, and for research purposes, a general mode where the input consists of a phone-graph also exists. A lexicon with multiple pronunciations for many words and a class bigram-grammar is used. The lexicon and grammar constraints are represented by a lexical graph, optimised for efficient lexical decoding. The decoding is performed in a two-pass search. The first pass is a Viterbi beam-search and the second is an A* stackdecoding search. Pruning-strategies and memory management in the two passes are discussed in the report. Several different output formats are available. Results can be reported either on the word or phoneme level with or without the time alignment information. Multiple hypotheses can be output either as standard Nbest lists or in a more compact word-graph format. Continuous speech recognition can be performed on a standard UNIX workstation in real-time with a lexicon of about 1000 words.
Hypoxaemia prevalence and management among children and adults presenting to primary care facilities in Uganda: a prospective cohort study (2021)

ABSTRACT Introduction Hypoxaemia (low blood oxygen) is common among hospitalised patients, increasing risk of death five-fold and requiring prompt detection and treatment. However, we know little about hypoxaemia prevalence in primary care and the role for pulse oximetry and oxygen therapy. This study assessed the prevalence and management of hypoxaemia at primary care facilities in Uganda. Methods Prospective cohort study in 30 primary care facilities in Uganda, Feb-Apr 2021. Clinical data collectors assessed blood oxygen level (SpO 2 ) of all acutely unwell children, adolescents, and adults, and followed up children aged under 15 years with SpO 2 &lt;93% to determine subsequent care and outcome. Primary outcome: proportion of children under 5 years of age with severe hypoxaemia (SpO 2 &lt;90%). Secondary outcomes: severe/moderate hypoxaemia (SpO 2 90-93%) by age/sex/complaint. Results Among children U5, the prevalence of severe hypoxaemia was 1.3% (95% CI 0.9 to 2.1); an additional 4.9% (3.9 to 6.1) had moderate hypoxaemia. Performing pulse oximetry according to World Health Organization guidelines exclusively on children with respiratory complaints would have missed 14% (3/21) of severe hypoxaemia and 11% (6/55) of moderate hypoxaemia. Hypoxaemia prevalence was low among children 5-14 years (0.3% severe, 1.1% moderate) and adolescents/adults 15+ years (0.1% severe, 0.5% moderate). A minority (12/27, 44%) of severely hypoxaemic patients were referred; 3 (12%) received oxygen. Conclusion Hypoxaemia is common among acutely unwell children under five years of age presenting to Ugandan primary care facilities. Routine pulse oximetry has potential to improve referral, management and clinical outcomes. Effectiveness, acceptability, and feasibility of pulse oximetry and oxygen therapy for primary care should be investigated in implementation trials. KEY QUESTIONS SUMMARY BOX What is already known? Hypoxaemia (low blood oxygen levels) is common among children and adults admitted to hospital with severe respiratory illness, increasing their risk of death at least 5-fold and requiring prompt detection and treatment. We know little about the prevalence of hypoxaemia in primary care, or whether pulse oximetry would improve decision-making or care for hypoxaemic patients. What are the new findings? In a Ugandan primary care context, hypoxaemia was common among acutely unwell children under five years of age and most were not referred to hospital for treatment. Hypoxaemia was uncommon among older children and adults presenting to Ugandan primary care facilities but prevalence increased with age into older adulthood. What do the new findings imply? Routine pulse oximetry screening may be warranted for acutely unwell children under five years of age, with a potential to improve referral, management and clinical outcomes. Effectiveness, acceptability, and feasibility of pulse oximetry and oxygen therapy for primary care should be investigated in further implementation trials.
A new soft ionization technique for mass spectrometry of complex molecules (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new soft ionization technique for mass spectrometry of complex moleculesC. R. Blakley, J. J. Carmody, and M. L. VestalCite this: J. Am. Chem. Soc. 1980, 102, 18, 5931–5933Publication Date (Print):August 1, 1980Publication History Published online1 May 2002Published inissue 1 August 1980https://pubs.acs.org/doi/10.1021/ja00538a050https://doi.org/10.1021/ja00538a050research-articleACS PublicationsRequest reuse permissionsArticle Views509Altmetric-Citations219LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
What Can We Learn from Chick Embryo Melanocytes? (1986)

Journal Article What Can We Learn from Chick Embryo Melanocytes? Get access John A. Brumbaugh, John A. Brumbaugh Search for other works by this author on: Oxford Academic Google Scholar William S. Oetting William S. Oetting Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 36, Issue 6, June 1986, Pages 381–387, https://doi.org/10.2307/1310260 Published: 01 June 1986
Transparent semi‐crystalline polymeric materials and their nanocomposites: A review (2020)

Abstract Optical transparency is an important property for a material, especially in certain fields like packaging, glazing, and displays. Existing commercial transparent polymeric materials are mostly amorphous. Semicrystalline polymers have often‐superior chemical resistance and mechanical properties particularly at elevated temperatures or after solid‐state drawing but they appear opaque or white in most cases. This review describes the present state‐of‐the‐art of methodologies of fabricating optically transparent materials from semicrystalline polymers. A distinction is made between isotropic, biaxially stretched, and uniaxially stretched semicrystalline polymers. Furthermore, some functionalities of transparent nanocomposites based on semicrystalline polymers are also discussed. This review aims to provide guidelines regarding the principles of manufacturing transparent high‐performance semicrystalline polymers and their nanocomposites for potential applications in fields like packaging, building, and construction, aerospace, automotive, and opto‐electronics.
Defining critical illness using immunological endotypes in patients with and without sepsis: a cohort study (2023)

Critically ill surgical patients express different and evolving immunological endotypes depending upon both their sepsis status and severity of their clinical course. Future studies will elucidate whether endotyping critically ill, septic patients can identify individuals for targeted therapeutic interventions to improve patient management and outcomes.