gebhart/patrepeval huggingface dataset:
Protein signature of human skin fibroblasts allows the study of the molecular etiology of rare neurological diseases (2020)

Abstract Background : The elucidation of pathomechanisms leading to the manifestation of rare (genetically caused) neurological diseases including neuromuscular diseases (NMD) represents an important step toward the understanding of the genesis of the respective disease and might help to define starting points for (new) therapeutic intervention concepts. However, these “discovery studies” are often limited by the availability of human biomaterial. Moreover, given that results of next-generation-sequencing approaches frequently result in the identification of ambiguous variants, testing of their pathogenicity is crucial but also depending on patient-derived material. Methods: Human skin fibroblasts were used to generate a spectral library using pH8-fractionation of followed by nano LC-MS/MS. Afterwards, Allgrove-patient derived fibroblasts were subjected to a data independent acquisition approach (DIA). In addition, proteomic signature of an enriched nuclear protein fraction was studied. Proteomic findings were confirmed by immunofluorescence in a muscle biopsy derived from the same patient and cellular lipid homeostasis in the cause of Allgrove syndrome was analysed by fluorescence (BODIPY-staining) and coherent anti-Stokes Raman scattering (CARS) microscopy. Results: To systematically address the question if human skin fibroblasts might serve as valuable biomaterial for (molecular) studies of NMD, we generated a protein library cataloguing 8280 proteins including a variety of such linked to genetic forms of motoneuron diseases, congenital myasthenic syndromes, neuropathies and muscle disorders. In silico -based pathway analyses revealed expression of a diversity of proteins involved in muscle contraction and such decisive for neuronal function and maintenance suggesting the suitability of human skin fibroblasts to study the etiology of NMD. Based on these findings, next we aimed to further demonstrate the suitability of this in vitro model to study NMD by a use case: the proteomic signature of fibroblasts derived from an Allgrove-patient was studied. Dysregulation of paradigmatic proteins could be confirmed in muscle biopsy of the patient and protein-functions could be linked to neurological symptoms known for this disease. Moreover, proteomic investigation of nuclear protein composition allowed the identification of protein-dysregulations according with structural perturbations observed in the muscle biopsy. BODIPY-staining on fibroblasts and CARS microscopy on muscle biopsy suggest altered lipid storage as part of the underlying disease etiology. Conclusions: our combined data reveal that human fibroblasts may serve as an in vitro system to study the molecular etiology of rare neurological diseases exemplified on Allgrove syndrome in an unbiased fashion.
Preservation of biological materials under desiccation (1997)

A number of life forms, including seeds, certain nematodes, bacterial and fungal spores, and cysts of certain crustaceans, show an ability to survive desiccation. The present article reviews the literature available on this subject and critically evaluates the evidence for various mechanisms that may be responsible for these phenomena. Specific mechanisms considered include vitrification (glass formation) by sugars and other polyhydroxy compounds that are accumulated by the desiccated structures, specific effects of polyhydroxy compounds on membranes, effect of "compatible solutes" on conformation of key proteins, as well as other biochemical mechanisms. The article presents potential applications relevant to food technology and to biotechnology and reviews the research required to materialize more effective use of desiccation in food and biopreservation.
High-Q whispering-gallery mode in the photonic crystal hexagonal cavity (2004)

Using the finite-difference time-domain calculations, we study whispering-gallery-like modes in photonic crystal air-bridge slab hexagonal defect cavities as good candidates for high quality-factor (Q) and small mode-volume (V) resonant modes. In the hexapole mode of a modified single-defect cavity, structural parameters are optimized to obtain very large Qs of even higher than 2 x 10<sup>6</sup> with small effective V of the order of cubic wavelength in material, the record value of theoretical Q/V. In addition, the H2-cavity whispering-gallery mode (WGM) is investigated and the defect geometry is modified to increase the Q of the WGM. By symmetrically distributing 12 nearest neighbor holes around the defect and controlling size of holes, it is possible to drastically increase the Q of >10<sup>5</sup> while preserving effective mode volume of the order of the cubic wavelength in material. We expect the WGMs in photonic crystal cavities are quite promising for low-loss photonic integrated circuit elements and high-efficiency quantum optical devices.
Beryllium Phosphonitrilates (1966)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBeryllium PhosphonitrilatesKay L. Paciorek and Reinhold H. KratzerCite this: Inorg. Chem. 1966, 5, 4, 538–541Publication Date (Print):April 1, 1966Publication History Published online1 May 2002Published inissue 1 April 1966https://pubs.acs.org/doi/10.1021/ic50038a009https://doi.org/10.1021/ic50038a009research-articleACS PublicationsRequest reuse permissionsArticle Views36Altmetric-Citations20LEARN 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
The Importance of Adding Short-Wave Infrared Bands for Forest Disturbance Monitoring in the Subtropical Region (2022)

Forest disturbance, such as harvest and fire, can cause a huge amount of carbon emission from soil to the atmosphere. Monitoring forest disturbance at a high spatial resolution is critical for soil carbon modeling. The short-wave infrared bands are important bands in monitoring forest disturbance. However, many high spatial resolution satellites do not contain the short-wave infrared bands in their band designs, and whether the lack of short-wave infrared (SWIR) bands will cause a large influence on forest disturbance monitoring remains unclear. This study aims to evaluate the values of adding SWIR bands in forest disturbance monitoring using the modified continuous monitoring of land disturbance (COLD) approach. Results showed that without the SWIR bands the accuracy of detecting forest disturbance will be reduced by 19–26%. The highest accuracy of modified COLD using the optimal band combination with SWIR bands was 76.3% for monitoring harvest and 86.6% for monitoring fire, while it decreased to 49.8% in detecting harvest and 67.6% in detecting fire without using any SWIR bands. The results demonstrated the importance of adding SWIR bands in forest disturbance monitoring and would guide users to select the satellite data with at least one SWIR band to monitor forest disturbance for improving the soil carbon modeling.
Nucleic acid vaccination primes hepatitis B virus surface antigen-specific cytotoxic T lymphocytes in nonresponder mice (1995)

The efficiency of different vaccination techniques to prime in vivo major histocompatibility complex class I-restricted murine cytotoxic T-lymphocyte (CTL) precursors to hepatitis B virus small surface antigen (HBsAg) was investigated. Mice were immunized either by injection of a low dose of recombinant HBsAg protein preparations (native HBsAg particles or denatured HBsAg monomers) without adjuvants, by infection with recombinant vaccinia virus carrying an HBsAg-encoding gene, or by intramuscular transfer of plasmid DNA encoding HBsAg under appropriate promoter control. In H-2d mice, an Ld-restricted, S28-39-specific CTL response was efficiently primed by all alternative vaccination techniques tested, but the most potent priming of class I-restricted CTL to HBsAg in vivo was observed with DNA immunization. Priming of anti-HBsAg CTL in H-2b mice was not detectable after infection with a recombinant vaccinia virus or after injection with exogenous recombinant HBsAg preparations. After DNA immunization, however, both Kb- and Db-restricted CTL reactivity to HBsAg emerged in H-2b mice. Hence, nucleic acid immunization revealed class I-restricted CTL responsiveness to HBsAg in a mouse strain previously considered to be a nonresponder at the CTL level. These results demonstrate that the simple technique of nucleic acid immunization not only is extremely efficient but also reveals an extended spectrum of potentially immunogenic epitopes of protein antigens.
Optimal error protection for real time image and video transmission (2004)

In this paper a novel and computationally inexpensive analytic mean square error (MSE) distortion rate (D-R) estimator for SPIHT which generates a nearly exact distortion rate (D-R) function for the 2D and 3D SPIHT algorithm is presented. The analytical formula is derived from the observations that for any bit-plane coder, the slope of the D-R curve is constant for each level of the bit plane. Furthermore the slope of D-R curve reduces by a factor proportional to the level of the bit plane. An application of the derived results is presented in the area of 2D SPIHT transmission employing a binary symmetric channel (BSC) and Reed Solomon (RS) forward error correction (FEC) codes. Utilizing our D-R estimate, we employ unequal error protection (UEP) and equal error protection (EEP) in order to minimize the end to end mean square error (MSE) distortion of the transform domain. UEP yields a significant performance gain relative to EEP only when the average number of parity bits for a group of packets is constrained. When both the source rate and channel code rate varied under a bit budget constraint, optimal UEP yields only a slight improvement over the optimal EEP. A major contribution of this paper is the simple and extremely accurate analytical D-R model which potentially improves upon pre-existing methodologies and applications that rely on an accurate and computationally inexpensive D-R estimate. Another important contribution is that the optimum EEP, which requires almost no header information and can easily be computed using our method, is only slightly worse than the optimum UEP.
Fast adaptive encoder for bi-level images (2002)

We present a new bi-level image compression coder that does not use arithmetic encoding, but whose performance is close to that of state-of-the-art coders such as JBIG, JBIG-2, and JB2. The proposed bi-level coder (BLC) uses two simple adaptation rules: the first to compute context-dependent probability estimates that control a pixel prediction module, and the second to adjust a run-length parameter in a run-length-Rice (RLR) coder. That's contrary to the usual approach where the context-dependent probability estimate controls both pixel prediction and adaptive entropy coding. Due to its simplicity, in many applications BLC may be a better choice than JBIG or JBIG-2.
Effect of oxygen inhalation at birth on the reduction of early postnatal mortality in pigs. (2001)

Asphyxia during delivery is considered a main cause of stillbirth in pigs, but piglets suffering from intermittent asphyxia during delivery are also less viable at birth and less prone to adapt to extrauterine life. In an effort to improve pig viability, one attractive solution would be to increase oxygen supply through oxygen inhalation by the newborn pig. The objective of this study was to test effects of oxygen inhalation immediately after birth on various physiological parameters and piglet survival. The experiment was performed on 252 Piétrain x Large White piglets, half of them reoxygenated immediately after birth. They were maintained during 20 min in a chamber where oxygen concentration was monitored at 40% and were then put back with the sow and the control pigs. Oxygen inhalation affected piglet metabolism. Through stimulation of oxidative metabolism (reduction of circulating levels of lactate) and lowering of the level of postnatal hypothermia (particularly for the lightest pigs), oxygen inhalation increased piglet viability and reduced mortality during the 1st d of life by 75% (2 vs 8%). No additional effects were observed during the following days and overall mortality between birth and weaning at 21 d was reduced from 12 to 8%.
Doppler Shift Estimation Based Channel Estimation for Orthogonal Time Frequency Space System (2021)

Orthogonal time frequency space (OTFS) is a multi-carrier technique where a time-varying channel can be converted into a time-invariant channel in the delay-Doppler (DD) domain through a two-dimensional transformation. In practical wireless systems, due to the non-biorthogonal waveforms, the inter-carrier interference (ICI) will bring up phase shifts related to Doppler shifts, so that the channel in the DD domain is no longer invariant. Moreover, the limited frame durations will lead to channel dispersion, which makes it more difficult to estimate Doppler shifts. However, existing channel estimation schemes for OTFS are unable to accurately estimate the Doppler shifts. In this paper, we propose a novel channel estimation scheme. Firstly, we estimate Doppler shifts by linear fitting based on the channel dispersion in the DD domain. Then we calculate the power of dispersion paths as combining coefficients to obtain channel fading. Simulation results show that the proposed scheme can significantly reduce the normalized mean square error compared with conventional schemes, especially if Doppler shifts are large.
0j.py: a software tool for low complexity proteins and protein domains (2001)

Low complexity proteins and protein domains have sequences which appear highly non-random. Over the years, these sequences have been routinely filtered out during sequence similarity searches because interest has been focused on globular proteins, and inclusion of these domains can severely skew search results. However, early work on these proteins and more recent studies of the related area of repeated protein sequences suggests that low complexity protein domains have function and therefore are in need of further investigation. 0j.py is a new tool for demarcating low complexity protein domains more accurately than has been possible to date. The paper describes 0j.py and its use in revealing proteins with repeated and poly-amino-acid peptides. Statistical methods are then employed to to examine the distribution of these proteins across species, while keyword clustering is used to suggest roles performed by proteins through the use of low complexity domains.
Autophagy is essential for cardiac morphogenesis during vertebrate development (2014)

Genetic analyses indicate that autophagy, an evolutionarily conserved lysosomal degradation pathway, is essential for eukaryotic differentiation and development. However, little is known about whether autophagy contributes to morphogenesis during embryogenesis. To address this question, we examined the role of autophagy in the early development of zebrafish, a model organism for studying vertebrate tissue and organ morphogenesis. Using zebrafish that transgenically express the fluorescent autophagy reporter protein, GFP-LC3, we found that autophagy is active in multiple tissues, including the heart, during the embryonic period. Inhibition of autophagy by morpholino knockdown of essential autophagy genes (including atg5, atg7, and becn1) resulted in defects in morphogenesis, increased numbers of dead cells, abnormal heart structure, and reduced organismal survival. Further analyses of cardiac development in autophagy-deficient zebrafish revealed defects in cardiac looping, abnormal chamber morphology, aberrant valve development, and ectopic expression of critical transcription factors including foxn4, tbx5, and tbx2. Consistent with these results, Atg5-deficient mice displayed abnormal Tbx2 expression and defects in valve development and chamber septation. Thus, autophagy plays an essential, conserved role in cardiac morphogenesis during vertebrate development.
S-217622, a SARS-CoV-2 main protease inhibitor, decreases viral load and ameliorates COVID-19 severity in hamsters (2022)

In parallel with vaccination, oral antiviral agents are highly anticipated to act as countermeasures for the treatment of the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Oral antiviral medication demands not only high antiviral activity but also target specificity, favorable oral bioavailability, and high metabolic stability. Although a large number of compounds have been identified as potential inhibitors of SARS-CoV-2 infection in vitro, few have proven to be effective in vivo. Here, we show that oral administration of S-217622 (ensitrelvir), an inhibitor of SARS-CoV-2 main protease (M<sup>pro</sup>; also known as 3C-like protease), decreases viral load and ameliorates disease severity in SARS-CoV-2-infected hamsters. S-217622 inhibited viral proliferation at low nanomolar to submicromolar concentrations in cells. Oral administration of S-217622 demonstrated favorable pharmacokinetic properties and accelerated recovery from acute SARS-CoV-2 infection in hamster recipients. Moreover, S-217622 exerted antiviral activity against SARS-CoV-2 variants of concern, including the highly pathogenic Delta variant and the recently emerged Omicron BA.5 and BA.2.75 variants. Overall, our study provides evidence that S-217622, an antiviral agent that is under evaluation in a phase 3 clinical trial (clinical trial registration no. jRCT2031210350), has remarkable antiviral potency and efficacy against SARS-CoV-2 and is a prospective oral therapeutic option for COVID-19.
Study of cohort-specific consent and patient control in phase I cancer trials. (1998)

PURPOSE To address the challenging ethical dilemmas created from the participation of advanced cancer patients in phase I trials, we assessed the feasibility of a clinical trial design that uses an interactive informed consent process in which patient-subjects can choose to become directly involved in decisions of dose escalation. PATIENTS AND METHODS Subjects were advanced cancer patients in the Hematology/Oncology Clinics at the University of Chicago who were eligible to participate in a phase I trial in which they underwent a three-step informed consent process that used cohort-specific consent and allowed them the option to choose their own doses of the chemotherapeutic agents under study, vinorelbine (NVB) and paclitaxel (TAX), within predetermined limits. NVB and TAX were administered in conventional 21- to 28-day cycles for two cycles while on study. Dose escalation occurred when a patient-subject chose a higher untested dose after they received information on all previously assessable patient-subjects. In addition to the phase I trial itself, a survey that consisted of structured interviews, which sought to evaluate patients' experiences with the interactive subject-choice phase I trial design and consent process, was conducted with participating subjects. The phase I trial itself sought to determine the associated toxicities of the agents under study. The survey results were compared with a similar survey of a matched control population of subjects who participated in other concurrently active conventional phase I trials at our institution. RESULTS Twenty-nine patient-subjects participated in the phase I trial, with 24 who agreed to and completed the survey interviews. Seventy-six percent of patient-subjects opted to choose their dose of the agents under study, and 28% chose the highest available doses. More than half of the patient-subjects (56%) felt some degree of comfort in being asked to choose their dose of chemotherapy, with 53% stating that being asked to choose their dose made them feel in control, fully informed, or content. However, there were no statistically significant improvements in objective measures of the informed consent process, which included surveyed subjects' stated understanding of either provided information about phase I trials and alternatives to trial participation or of the research purpose of phase I trials. By making choices, the group of patients in the interactive subject choice trial changed the size of the dose cohorts and modified the process of dose escalation in this phase I study. CONCLUSION Although complex, our innovative phase I trial design is feasible. In addition to the use of cohort-specific consent, the trial design may reduce the magnitude of many of the commonly recognized ethical dilemmas associated with this form of clinical research, which include difficulties with information provision and the understanding of possible risks and benefits of phase I trial participation, through direct subject involvement in research decision making by otherwise potentially vulnerable cancer patients.
Operational Limits of Measuring while Drilling in Florida Limestone for Geotechnical Site Characterization (2021)

Rock coring is an essential method of geotechnical site characterization for foundations supported by rock, in which three possible phases of operation exist: inefficient, optimized, and destructive. When operating within the optimized phase, core recoveries and the rock quality designation reflect the strata encountered. However, the optimized phase is rarely achieved in practice, leading to deficiencies in strength assessment and geotechnical site characterization. This paper identifies the operational limits that separate each phase of rock coring by using measuring while drilling (MWD) and quantifies the increased energy that results from an inadequate depth of cut (Phase 1), the effects of breaking rock particles into smaller sizes, and the damage that occurs to core specimens from increased frictional resistance (Phase 3), as well as the effect rock strength and bit geometry have on mechanical efficiency. Drilling parameter interdependencies are discussed and detailed guidelines to assess rock strength in situ via MWD are provided. Finally, recommended coring guidelines are established through MWD which optimize the quantity and quality of strength assessments collected to improve geotechnical site characterization.
Identification of the Antibacterial Compound Produced by the Marine Epiphytic Bacterium Pseudovibrio sp. D323 and Related Sponge-Associated Bacteria (2011)

Surface-associated marine bacteria often produce secondary metabolites with antagonistic activities. In this study, tropodithietic acid (TDA) was identified to be responsible for the antibacterial activity of the marine epiphytic bacterium Pseudovibrio sp. D323 and related strains. Phenol was also produced by these bacteria but was not directly related to the antibacterial activity. TDA was shown to effectively inhibit a range of marine bacteria from various phylogenetic groups. However TDA-producers themselves were resistant and are likely to possess resistance mechanism preventing autoinhibition. We propose that TDA in isolate D323 and related eukaryote-associated bacteria plays a role in defending the host organism against unwanted microbial colonisation and, possibly, bacterial pathogens.