gebhart/patrepeval huggingface dataset:
Chickens, more than humans, focus the diversity of their immunoglobulin genes on the complementarity-determining region but utilise amino acids, indicative of a more cross-reactive antibody repertoire (2022)

The mechanisms of B-cell diversification differ greatly between aves and mammals, but both produce B cells and antibodies capable of supporting an effective immune response. To see how differences in the generation of diversity might affect overall repertoire diversity, we have compared the diversity characteristics of immunoglobulin genes from domestic chickens to those from humans. Both use V(D)J gene rearrangement and somatic hypermutation, but only chickens use somatic gene conversion. A range of diversity analysis tools were used to investigate multiple aspects of amino acid diversity at both the germline and repertoire levels. The effect of differing amino acid usages on antibody characteristics was assessed. At both the germline and repertoire levels, chickens exhibited lower amino acid diversity in comparison to the human immunoglobulin genes, especially outside of the complementarity-determining region (CDR). Chickens were also found to possess much larger and more hydrophilic CDR3s with a higher predicted protein binding potential, suggesting that the antigen-binding site in chicken antibodies is more flexible and more polyreactive than that seen in human antibodies.
Clinical characteristics of neonates with coronavirus disease 2019 (COVID-19): a systematic review (2020)

<title>Abstract</title> This study aimed to summarize the existing literature on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in newborns to clarify the clinical features and outcomes of neonates with COVID-19. A systematic search was performed in PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), Wanfang Data, and VIP databases from January 1, 2019 to April 30, 2020. The references of relevant studies were also searched. A descriptive summary was organized by aspects of clinical presentations (symptoms, laboratory examinations, and imaging) and outcomes. We identified 14 studies reporting 18 newborns with COVID-19. The most common clinical manifestations were fever (62.5%), shortness of breath (50.0%), diarrhea/vomiting/feeding intolerance(43.8%), cough (37.5%), dyspnea (25.0%), and nasal congestion/runny nose/sneeze(25.0%). Atypical symptoms included jaundice and convulsion. Lymphocyte numbers decreased in 5 cases, and radiographic findings were likely to show pneumonia. All newborns recovered and discharged from the hospital, and there was no death.<bold>Conclusion:</bold><italic> </italic>Clinical symptoms of neonatal SARS-CoV-2 infection are atypical, most of them are mild. Up to now, the prognosis of newborns is good, and there is no death. Intrauterine vertical transmission is possible, but confirmed evidence is still lacking. The Long-term follow-up of potential influences of SARS-CoV-2 infection on neonates need further exploration.
Beatbox Music Phone: Gesture-based Interactive Mobile Phone using a Tri-axis Accelerometer (2006)

In this paper, we propose gesture-based interaction methods using a tri-axis accelerometer for mobile devices. The algorithms for the gesture recognition and the shaking detection are suggested for gesture interaction. They have been implemented in the commercialized mobile phone (model name: SCH-S310). The mobile phone recognizes digits from 1 to 9 and five symbols written in the air. It detects the shaking motion to initiate commands for the gesture interactive games and musical instrument applications. We used the signals from a tri-axis accelerometer to recognize the gestures directly without trajectory estimation. In the experimental study, we achieved 97.01% of average recognition rate for a set of eleven gestures. The rate is cross validated from a whole data set of 3082 gestures from 100 users. The performance of the shaking detection methods shows that gesture-based interaction can be used as input methods of games and musical instrument applications for entertainment.
em In silico em modeling techniques for predicting the tertiary structure of human H4 receptor (2015)

First cloned in 2000, the human Histamine H4 Receptor (hH4R) is the last member of the histamine receptors family discovered so far, it belongs to the GPCR super-family and is involved in a wide variety of immunological and inflammatory responses. Potential hH4R antagonists are proposed to have therapeutic potential for the treatment of allergies, inflammation, asthma and colitis. So far, no hH4R ligands have been successfully introduced to the pharmaceutical market, which creates a strong demand for new selective ligands to be developed. in silico techniques and structural based modeling are likely to facilitate the achievement of this goal. In this review paper we attempt to cover the fundamental concepts of hH4R structure modeling and its implementations in drug discovery and development, especially those that have been experimentally tested and to highlight some ideas that are currently being discussed on the dynamic nature of hH4R and GPCRs, in regards to computerized techniques for 3-D structure modeling.
Secreted Semaphorins Modulate Synaptic Transmission in the Adult Hippocampus (2005)

Modulation of synaptic activity is critical for neural circuit function and behavior. The semaphorins are a large, phylogenetically conserved protein family with important roles in neural development. However, semaphorin function in the adult brain has yet to be determined. Here, we show that the coreceptors for secreted semaphorins, the neuropilins, are found at synapses and localize to molecular layers of the adult mouse hippocampus and accessory olfactory cortex. Moreover, application of the secreted semaphorin Sema3F to acute hippocampal slices modulates both the frequency and amplitude of miniature EPSCs in granule cells of the dentate gyrus and pyramidal neurons of CA1. Finally, we show that mice lacking Sema3F are prone to seizures. These results suggest a novel role for semaphorins as synaptic modulators and illustrate the diverse repertoire of these guidance cues in both the formation and function of neural circuits.
T Cells Can Bind Antigen via Cytophilic IgM Antibody Made by B Cells (1973)

Abstract The specificity of cell-mediated immune responses presupposes the existence of an antigen recognition unit associated with those cells responsible for this type of immunity. Evidence is accumulating which indicates the presence of immunoglobulins on thymus-dependent lymphocytes (T cells)2 and suggests that these may represent the recognition units (1–10). Much of the supporting evidence was obtained from studies in which anti-immunoglobulin reagents inhibited antigen binding by T cells as detected by direct (autoradiography and erythrocyte rosette formation) and indirect (e.g., highly radioactive antigen-induced “suicide”) techniques. Most of these studies were done in mice; in all instances the T cells studied had been associated in vivo with bone marrow dependent (B) cells and their immunoglobulin products. Agammaglobulinemic (Aγ) chickens represent an animal model particularly well suited to studies involving T lymphocytes since they completely lack B cells and circulating immunoglobulins but have normal T cell development and cell mediated immunity. Efforts in this and other laboratories to detect antigen binding to T cells from Aγ birds by rosette formation, bacterial adherence and autoradiography have been unsuccessful (11–14). In the present experiments thymocytes and peripheral blood lymphocytes from Aγ chickens were investigated for their ability to form rosettes with sheep erythrocytes (SRBC) before and after incubation in primary immune sera from normal chickens.
Quantitative effect of target translation on small RNA efficacy reveals a novel mode of interaction (2014)

Small regulatory RNAs (sRNAs) in bacteria regulate many important cellular activities under normal con-ditions and in response to stress. Many sRNAs bind to the mRNA targets at or near the 5 ′ untranslated re-gion (UTR) resulting in translation inhibition and ac-celerated degradation. Often the sRNA-binding site is adjacent to or overlapping with the ribosomal bind-ing site (RBS), suggesting a possible interplay be-tween sRNA and ribosome binding. Here we combine quantitative experiments with mathematical model-ing to reveal novel features of the interaction be-tween small RNAs and the translation machinery at the 5′UTR of a target mRNA. By measuring the re-sponse of a library of reporter targets with varied RBSs, we find that increasing translation rate can lead to increased repression. Quantitative analysis of these data suggests a recruitment model, where bound ribosomes facilitate binding of the sRNA. We experimentally verified predictions of this model for the cell-to-cell variability of target expression. Our findings offer a framework for understanding sRNA silencing in the context of bacterial physiology.
Flow-Field Geometry Effect on H2–Iron Redox Flow Battery (2020)

The redox flow battery is getting intense attention these days as one of the most promising systems to store energy generated from weather-dependent renewable energy sources such as solar and wind energies. In this research, the geometry-related performance of the hydrogen–iron redox flow battery is analyzed with five different flow-field geometries (parallel, serpentine, crisscross, interdigitated, and porous) to determine the best geometry leading to the maximum cell power and fuel efficiency. Diffusion-dominant flow-by mode, convection-dominant flow-through mode, and the hybrid combining both modes are investigated in detail to understand the characteristic transport modes of reactive species and underlying flow physics. In particular, the effects of the flow geometries are analyzed with respect to system-based as well as cell-based performance. It is found that the best net power gain is achieved from the porous flow field, which has excellent fuel utilization and cell power with a low electrolyte supply rate.
Multifaceted Recognition of Vertebrate Rev1 by Translesion Polymerases ζ and κ (2012)

Translesion synthesis is a fundamental biological process that enables DNA replication across lesion sites to ensure timely duplication of genetic information at the cost of replication fidelity, and it is implicated in development of cancer drug resistance after chemotherapy. The eukaryotic Y-family polymerase Rev1 is an essential scaffolding protein in translesion synthesis. Its C-terminal domain (CTD), which interacts with translesion polymerase ζ through the Rev7 subunit and with polymerases κ, ι, and η in vertebrates through the Rev1-interacting region (RIR), is absolutely required for function. We report the first solution structures of the mouse Rev1 CTD and its complex with the Pol κ RIR, revealing an atypical four-helix bundle. Using yeast two-hybrid assays, we have identified a Rev7-binding surface centered at the α2-α3 loop and N-terminal half of α3 of the Rev1 CTD. Binding of the mouse Pol κ RIR to the Rev1 CTD induces folding of the disordered RIR peptide into a three-turn α-helix, with the helix stabilized by an N-terminal cap. RIR binding also induces folding of a disordered N-terminal loop of the Rev1 CTD into a β-hairpin that projects over the shallow α1-α2 surface and creates a deep hydrophobic cavity to interact with the essential FF residues juxtaposed on the same side of the RIR helix. Our combined structural and biochemical studies reveal two distinct surfaces of the Rev1 CTD that separately mediate the assembly of extension and insertion translesion polymerase complexes and provide a molecular framework for developing novel cancer therapeutics to inhibit translesion synthesis.
Gate-count estimates for performing quantum chemistry on small quantum computers (2014)

As quantum computing technology improves and quantum computers with a small but non-trivial number of N > 100 qubits appear feasible in the near future the question of possible applications of small quantum computers gains importance. One frequently mentioned application is Feynman's original proposal of simulating quantum systems, and in particular the electronic structure of molecules and materials. In this paper, we analyze the computational requirements for one of the standard algorithms to perform quantum chemistry on a quantum computer. We focus on the quantum resources required to find the ground state of a molecule twice as large as what current classical computers can solve exactly. We find that while such a problem requires about a ten-fold increase in the number of qubits over current technology, the required increase in the number of gates that can be coherently executed is many orders of magnitude larger. This suggests that for quantum computation to become useful for quantum chemistry problems, drastic algorithmic improvements will be needed.
Retraction Note: Novel life history strategy in a deep sea fish challenges assumptions about reproduction in extreme environments (2020)

Editor's Note: this Article has been retracted; the Retraction Note is available at https://doi.org/10.1038/s41598-020-75408-8 .
The Disulfide Linkage and the Free Sulfhydryl Accessibility of Acyl-Coenzyme A:Cholesterol Acyltransferase 1 As Studied by Using mPEG5000-Maleimide (2005)

Acyl-coenzyme A:cholesterol acyltransferase (ACAT) is a membrane protein located in the endoplasmic reticulum (ER). It plays important roles in cellular cholesterol homeostasis. Human ACAT1 (hACAT1) contains nine cysteines (C). To quantify and map its disulfide linkage, we performed thiol-specific modifications by mPEG(5000)-maleimide (PEG-mal) and iodoacetamide (IA) under denatured condition, using extracts that contain wild-type or various single C to A mutant hACAT1s. With the wild-type enzyme, seven Cs could be modified before dithiothreitol (DTT) treatment; nine Cs could be modified after DTT treatment. With the C528A or the C546A enzyme, all eight Cs could be modified before or after DTT treatment. With all other remaining single C to A mutant enzymes, six Cs could be modified before DTT treatment, and eight Cs could be modified after DTT treatment. We next performed Lys-C protease digestion on hACAT1 with a hemagglutinin (HA) tag at the C-terminus. The digests were treated with or without DTT and analyzed by SDS-PAGE and Western blotting. The two predicted C-terminal fragments (K496-K531 and N532-F550-HA tag) were trapped as a single peptide band, but only when the digests were treated without DTT. Thus, C528 and C546 near the enzyme's C-terminus form a disulfide. PEG-mal is impermeable to ER membranes. We used PEG-mal to map the localizations of the seven free sulfhydryls and the disulfide bond of hACAT1 present in microsomal vesicles. The results show that C92 is located on the cytoplasmic side of the ER membrane and the disulfide is located in the ER lumen, while all other free Cs are located within the hydrophobic region(s) of the enzyme.
A Cautionary Note on the Zagarola and Smits Similarity Parameter for the Turbulent Boundary Layer (2015)

Zagarola and Smits developed an empirical velocity parameter for scaling the outer region of the turbulent boundary layer velocity profile that has been widely applied to experimental datasets. Plots of the scaled defect profiles indicate that most datasets display similar-like behavior using the Zagarola and Smits scaling parameter. In the work herein, it is shown that the common practice of finding similarity behavior using the defect profile is often incomplete in the sense that not all of the criteria for similarity have been checked for compliance. When full compliance is checked, it is found that most of the datasets which display defect similarity do not satisfy all the criteria required for similarity. The nature of this contradiction and noncompliance is described in detail. It is shown that the original datasets used by Zagarola and Smits display this flawed similarity behavior. Hence, a careful reassessment of any claims in the literature is required for those groups that attempted to use the defect profile and the Zagarola and Smits type of velocity scaling parameter to assert similarity of the velocity profile.
Pleural carcinosis confirmed by adjuvant cytological methods: A case report (1998)

We describe a case of a 43-yr-old woman presenting a progressive pleural effusion. The patient was known to have an acute myeloid leukemia in complete remission after allogenic bone marrow transplantation. Suspicion of pleural carcinosis was raised cytologically and confirmed by immunocytochemistry, DNA-cytometry, and atomic force microscopy. We emphasize the use of these additional methods for the distinction of adenocarcinoma cells in effusions from reactive mesothelial cells. Diagn. Cytopathol. 1998;19:370–374. © 1998 Wiley-Liss, Inc.
Low cost cataract detection system using smart phone (2015)

Cataracts are blinding retina of millions of people. Current test Cataract detection from retinal is expensive using fundus camera as the detection is the key reason for this is not portable, needs an expert to perform the operation. This paper presents a low-cost smartphone based on smart systems integration and micro lenses allows patients in remote areas to have regular eye checks and the innovative development of disease diagnosis. The official mobile diagnostic system to analysis of retinal images taken by microscopic lens to identify retinal disease conditions. Firstly we know that there are not very good medical facilities in remote areas and clinic in those area could not afford very costly machines which are required for the detection of cataract. Secondly time taken by the machine to detect cataract is more doctor could not attend more number of patience. So if we use smartphone by attaching perfect focal length lens with android application this will save cost and time.
Breves comentários ao art. 10 da Lei n. 7.347/85 (2006)

RESUMO Analisa o crime previsto no art. 10 da Lei n. 7.347/85, que trata da desobediencia a requisicao emanada pelo Ministerio Publico de dados tecnicos indispensaveis ao ajuizamento da acao civil, e discorre sobre os elementos tipicos necessarios a configuracao do tipo penal. Alega que esse crime se sintoniza com a importância do Ministerio Publico na defesa dos direitos metaindividuais e no prestigio dado a instituicao para tal fim, o que se apreende nao somente da Constituicao, mas tambem de varios dispositivos legais. Assim, o estudo do tipo penal em comento adquire relevo significativo, pois, uma vez que protege um direito fundamental, deve ser aplicado com apuro e tecnica. PALAVRAS-CHAVE Direito Penal; Lei n. 7.347/85 – art. 10; Ministerio Publico; inquerito civil; acao civil publica; tipo penal; crime. ABSTRACT The author analyses the crime set forth in article 10 of Law n. 7,347/85, which deals with the disobedience to the order, issued by the Public Prosecution Service, to get technical data regarded as essential to the civil action proceeding. Moreover, he discourses on typical elements necessary to establish the criminal classification. He states that this crime is in tune with the importance of the Public Prosecution Service for the defense of the meta-individual rights and the prestige given to the institution viewing such aim, which may be learnt not only from the Brazilian Constitution, but also from several legal provisions. Therefore, the study of the referred criminal classification acquires significant relevance, for, inasmuch as it protects a fundamental right, it must be enforced with accuracy and technique. KEYWORDS Criminal Law; Law n. 7,347/85 – article 10; Public Prosecution Service; civil inquiry; public civil action; criminal classification; crime.
Multipin technology in the preparation and screening of peptide libraries. (1994)

Peptide libraries are relatively new sources of enormous numbers of unique compounds, fodder for the mill of drug discovery programs. Their enormous diversity derives from vast numbers of combinations of a small number of monomers (Geysen et al., 1986). For example, a complete hexapeptide library synthesized from just 10 monomers (amino acids) has one million unique compounds in it. In principle, other types of combinatorial libraries can have equally vast numbers of members; for example, the monomers can be N-acyl glycines, giving rise to the so-called "peptoids" (Simon et al., 1992); or the monomers could be monosaccharides or nucleotides.
Restriction endonuclease analysis of chloroplast DNA from A-genome diploid species of rice. (1988)

Relationships between chloroplast genomes (=ctDNAs) from diploid, A- genome species of rice (Oryza spp.) were established using length differences in restriction fragments of ctDNAs. Five out of 11 endonucleases used revealed differences in ctDNA fragment lengths among 19 accessions of the cultivated species, O. sativa and O. glaberrima. A larger sample of ctDNAs from 66 accessions of both wild and cultivated species were analyzed with three of those five endonucleases, resulting in the identification of nine types of chloroplast genome. In the wild species, the four geographical forms of O. perennis were found to contain one (African), one (Oceanian), three (Asian), and four (American) types, whereas O. breviligulata contained only one type of chloroplast genome. In the cultivated species, the three ecospecies of O. sativa contained one (Japonica and Javanica) and three (Indica) types, whereas O. glaberrima contained one type of chloroplast genome. The latter type was shared exclusively with O. breviligulata, suggesting that the former species had been domesticated from the latter. Two chloroplast genome types were shared by O. sativa and the Asian form of O. perennis, suggesting that the former species had derived from the latter via two domestication events.
All-magnetic magnetoresistive random access memory based on four terminal mCell device (2015)

Magnetoresistive random access memory (MRAM) is a promising candidate to enable fast, non-volatile storage on chip. In this paper, we present an MRAM design where each bitcell is comprised entirely of four-terminal magnetic devices (“mCells”) with no CMOS access transistors. We show that this design can achieve significant energy and area savings compared to the standard one transistor-one magnetic tunnel junction (1T1MTJ) bitcell based design. We estimate a write energy of ≈5 fJ/bit based on bitline and wordline voltages that operate at less than 100 mV with projected area smaller than that possible with aggressively scaled 10 nm node FinFETs in the 1T1MTJ design.
Didox (3,4-Dihydroxybenzohydroxamic acid) is a potent anti-oxidant and anti-inflammatory compound (35.17) (2010)

Abstract Didox (3,4-Dihydroxybenzohydroxamic acid) is a synthetic antioxidant and one of the most potent ribonucleotide reductase inhibitors developed to date. Little is known about the potential for Didox as an anti-inflammatory agent. After an analysis of more than 200 oxidative stress- and inflammatory-associated genes in mouse RAW264.7 macrophages we show that Didox significantly lowers LPS-induced expression of inflammatory genes (iNOS, IL-1α, IL-1β, IL-6, TNF-α, NF-KB, Cox-2, p38α, TLR4, GM-CSF, G-CSF, CCL2, CCL4, others), while upregulating expression levels of anti-oxidant and anti-inflammatory genes (Catalase, glutathione peroxidase, IL-10, superoxide dismutase, and peroxiredoxins, others). In addition, Didox dose-dependently inhibits LPS-induced IL-6 secretion and nitric oxide production. Buthionine Sulfoximine- and LPS-induced ROS production are also suppressed by Didox. We also show that phagocytosis of yeast particles is decreased as well. In terms of cellular signaling, Didox prevents NF-KB activation and translocation of NF-kappa beta p65 subunits in LPS-treated cells. These results suggest that the mechanism behind anti-oxidant and anti-inflammatory properties of Didox may be mediated, at least in part, via modulation of NF-kappa beta signaling. Didox may, therefore, may hold promise in managing chronic diseases exacerbated by LPS-induced oxidative stress and inflammation in macrophage-mediated inflammation.