gebhart/patrepeval huggingface dataset:
The X chromosome and male infertility (2019)

Abstract The X chromosome is a key player in germ cell development, as has been highlighted for males in previous studies revealing that the mammalian X chromosome is enriched in genes expressed in early spermatogenesis. In this review, we focus on the X chromosome’s unique biology as associated with human male infertility. Male infertility is most commonly caused by spermatogenic defects to which X chromosome dosage is closely linked; for example, any supernumerary X chromosome as in Klinefelter syndrome will lead to male infertility. Furthermore, because males normally only have a single X chromosome and because X-linked genetic anomalies are generally only present in a single copy in males, any loss-of-function mutations in single-copy X-chromosomal genes cannot be compensated by a normal allele. These features make X-linked genes particularly attractive for studying male spermatogenic failure. However, to date, only very few genetic causes have been identified as being definitively responsible for male infertility in humans. Although genetic studies of germ cell-enriched X-chromosomal genes in mice suggest a role of certain human orthologs in infertile men, these genes in mice and humans have striking evolutionary differences. Furthermore, the complexity and highly repetitive structure of the X chromosome hinder the mutational analysis of X-linked genes in humans. Therefore, we conclude that additional methodological approaches are urgently warranted to advance our understanding of the genetics of X-linked male infertility.
Stimulation of reactive astrogliosis in vivo by extracellular adenosine diphosphate or an adenosine A<sub>2</sub> receptor agonist (1994)

Adenosine and its nucleotides adenosine triphosphate (ATP) and adenosine diphosphate (ADP) stimulate the proliferation of brain astrocytes in vitro and augment the effects of other growth factors. Following brain injury, hypoxia, or around solid tumors with necrotic centers, such as glioblastoma multiformes, high concentrations of adenine nucleotides and adenosine are released into the extracellular space; extracellular adenosine concentrations can rise 30-100-fold to a concentration in excess of 100 microM. Increased concentrations of extracellular adenosine and adenine nucleotides may contribute to reactive astrocytic proliferation following brain injury. To test this hypothesis, adenosine, an adenosine analog 5'-(N-cyclopropyl)-carboxamidoadenosine (CPCA), or ADP was micro-injected into rat cortex. The number of glial fibrillary acidic protein-immunopositive cells was compared between the treated and contralateral saline-injected hemispheres. Within 48 hr, astrocyte density around the CPCA (100 microM) infusion site was almost double that around the control saline infusion site. In hemispheres into which CPCA was infused, there was an increase in astrocytes in the subpial region along fiber tracts and around blood vessels, characteristic of Scherer's secondary structures found in association with malignant astrocytic brain tumors. The increased astrogliosis elicited by CPCA was abolished by coinfusion of the adenosine A2 receptor antagonist 1,3-dipropyl-7-methylxanthine (DPMX). While microinjection of adenosine (1 mM) failed to stimulate astrogliosis, microinjection of ADP (500 microM) also resulted in a significant reactive astrogliosis and accumulation of astrocytes similar to Scherer's secondary structures.(ABSTRACT TRUNCATED AT 250 WORDS)
Associative Embedding: End-to-End Learning for Joint Detection and\n Grouping (2016)

We introduce associative embedding, a novel method for supervising\nconvolutional neural networks for the task of detection and grouping. A number\nof computer vision problems can be framed in this manner including multi-person\npose estimation, instance segmentation, and multi-object tracking. Usually the\ngrouping of detections is achieved with multi-stage pipelines, instead we\npropose an approach that teaches a network to simultaneously output detections\nand group assignments. This technique can be easily integrated into any\nstate-of-the-art network architecture that produces pixel-wise predictions. We\nshow how to apply this method to both multi-person pose estimation and instance\nsegmentation and report state-of-the-art performance for multi-person pose on\nthe MPII and MS-COCO datasets.\n
1,2-Rearrangements of β-Nitrogen-Substituted (Porphyrinato)rhodium(III) Ethyls (2005)

(Porphyrinato)rhodium(III) ethyls containing β-nitrogen substituents have been showed to undergo clean, thermal 1,2-rearrangements into the α-nitrogen-substituted rhodium ethyls. The rates and the equilibrium positions were found to be dependent on the electronic nature of the N substituents. Complexes 1a−3a were characterized by X-ray crystallography.
The Total Synthesis of Antrimycin D<sub>v</sub>; III:<sup>1</sup>Construction of the Protected Hexapeptide and Deprotection (1993)

In the preceding communication we described the synthesis of tetrahydropyridazine-3-carboxylic acids and their incorporation into peptides. We have also prepared the tripeptide 2 which is contained in the antibiotic antrimycin Dv 15. We now report on the preparation of the building blocks 1 and 4 and their coupling with 2 to give the protected antrimycin Dv 14. The deprotection of this heptapeptide constitutes the total synthesis of antrimycin Dv.
The two single-strand cleavages at each end of Tn10 occur in a specific order during transposition. (1995)

During Tn10 transposition, the element is excised from the donor site by double-strand cleavages at the two transposon ends. Double-strand cleavage is a central step in the nonreplicative transposition reaction of many transposons in both prokaryotes and eukaryotes. Evidence is presented to show that the Tn10 double-strand cut is made by an ordered, sequential cleavage of the two strands. The transferred strand is cut first, and then the nontransferred strand is cleaved. The single-strand nicked intermediate is seen to accumulate when Mn2+ is substituted for Mg2+ in the reaction or when certain mutant transposases are used. The fact that the transferred strand is cleaved before the non-transferred strand implies that the order of strand cleavages is not the determining factor that precludes a replicative mechanism of transposition.
Effect of Homogenization Pressure and Oil Load on the Emulsion Properties and the Oil Retention of Microencapsulated Basil Essential Oil (<i>Ocimum basilicum</i>L.) (2012)

Abstract The objective of this work was to evaluate the influence of oil concentration and homogenization pressure on the emulsion and particle properties during the microencapsulation of basil essential oil by spray drying, using gum arabic as the wall material. Experiments were planned according a 22 rotational central composite design. The independent variables were oil concentration with respect to total solids (10–25%) and homogenization pressure (0–100 MPa). Emulsions were analyzed for droplet mean diameter, stability, and viscosity, and particles were analyzed for oil retention, moisture content, particle size, and morphology. Emulsion viscosity was not affected by any of the independent variables. The increase in the homogenization pressure from 0 to 100 MPa resulted in smaller emulsion droplet size (down to 0.40 µm) and, consequently, higher oil retention (up to 95%). On the other hand, higher oil loads (25%) resulted in poorer oil retention (51.22%). Microencapsulation of basil essential oil using gum arabic as the wall material proved to be a suitable process to obtain powdered basil essential oil, presenting great oil retention with the use of lower oil concentration and higher homogenization pressure. Keywords: Basil essential oilEmulsion propertiesGum arabicMicroencapsulationSpray drying ACKNOWLEDGMENTS The authors thank CNPq and FAPESP for financial support. Notes Note: Information provided by Linax Essential Oil Extraction. a Particle mean diameter was not a variable studied in the experimental design for response surface methodology. Means with the same lowercase letter did not differ significantly at P ≤ 0.05. Means with the same uppercase letter did not differ significantly at P ≤ 0.05. NS = Nonsignificant.
An atypical spontaneous song by Abbott's Babbler Trichastoma abbotti (2011)

The jungle babblers Timaliidae as a whole are renowned vocalists, more easily identified by their collectively varied songs than by their muted plumages. Surprisingly, the ornithological literature is incomplete concerning the repertoires of individual babbler species, as well as for noting regional (or racial) differences. The song of the Abbott's Babbler Trichastoma abbotti in south-eastern Sumatra has recently been the subject of a note in Kukila (Nash & Hash 1985), describing the full adult song of the male bird, and the duelling call notes of the female. Further studies of this species by the authors have revealed an unusual additional song by the male, a ten-note spontaneous 'foraging' song. This song was recorded in the Padang-Sugihan Wildlife Reserve, South Sumatra province, at approximately 0745 hrs. on 12 September 1985, in riverine swamp forest. The recorded song was examined on a Unigon 4500 Uniscan Spectrum Analyzer, and the sonogram was made on a Kay Digital Sono-Graph 7800 set to a wide (300 Khz) band range.
A Dose-Ranging Study of Lecithin in the Treatment of Primary Degenerative Dementia (Alzheimer Disease) (1982)

BRINKMAN, SAMUEL D. PHD; POMARA, NUNZIO MD; GOODNICK, PAUL J. MD; BARNETT, NEAL MA; DOMINO, EDWARD F. MD Author Information
Classic data structures in C (1994)

Part 1 Terms, tools and technology: engineering software - responsibility-driven design, programming from reusable components, problem solving heuristics, chapter summary creating software components - classes, streams, chapter summary algorithms - descriptions of behaviour - recipes as algorithms, printing integers, integer exponents, greatest common divisor, chapter summary. Part 2 Analysis, algorithms and abstractions: strings - an example ADT - primitive strings, the string data abstraction, pattern matching, chapter summary classification of collections vectors and component reuse - templates, simple vectors, techniques for software reuse, other vector variations, function templates, chapter summary inheritance - power through polymorphism - static and dynamic types, frameworks and virtual methods, varieties of inheritance, iterators, forms of polymorphism, the slicing problem, chapter summary lists - a dynamic data structure - simple lists, list iterators, application - polynomial arithmetic, ordered lists, self-organizing lists, double ended lsits, other common variations, application - free lists, chapter summary stacks and queues - higher level abstractions - the abstract classes stack and queue, stacks, application - RPN calculator, application - coversion of infix to postfix, queues, application - breadth first search, application - a framework for backtracking, chapter summary trees - a nonlinear data structure - binary trees, operator precedence parsing, tree traversals, binary tree representation of general trees, chapter summary searching - divide and conquer, binary search, ordered vectors, binary search trees, AVL trees, application - tree sort, finding the Nth largest, chapter summary priority queues - heaps, skew heaps, application - discrete event-driven simulation, chapter summary hash tables - collision resolution using buckets, asymptotic analysis of hash table operations, hash table iterators, application - bucket sorting, hash functions, chapter summary sets and bags - unordered collections - set operations, bit vector sets, the abstract set operations, building sets from hash tables, chapter summary dictionaries and tables - associations, dictionaries as lists of associations, ordered dictionaries, dictionaries as hash tables, chapter summary graphs - adjacency matrix representation, edge list representation, weighted adjacency matrix, labelled edge list representation, finite automata, chapter summary files - external collections.
Monitoring and managing microbes in aquaculture – Towards a sustainable industry (2016)

Microorganisms are of great importance to aquaculture where they occur naturally, and can be added artificially, fulfilling different roles. They recycle nutrients, degrade organic matter and, occasionally, they infect and kill the fish, their larvae or the live feed. Also, some microorganisms may protect fish and larvae against disease. Hence, monitoring and manipulating the microbial communities in aquaculture environments hold great potential; both in terms of assessing and improving water quality, but also in terms of controlling the development of microbial infections. Using microbial communities to monitor water quality and to efficiently carry out ecosystem services within the aquaculture systems may only be a few years away. Initially, however, we need to thoroughly understand the microbiomes of both healthy and diseased aquaculture systems, and we need to determine how to successfully manipulate and engineer these microbiomes. Similarly, we can reduce the need to apply antibiotics in aquaculture through manipulation of the microbiome, i.e. by the use of probiotic bacteria. Recent studies have demonstrated that fish pathogenic bacteria in live feed can be controlled by probiotics and that mortality of infected fish larvae can be reduced significantly by probiotic bacteria. However, the successful management of the aquaculture microbiota is currently hampered by our lack of knowledge of relevant microbial interactions and the overall ecology of these systems.
Aspect-Based Sentiment Analysis Using a Hybridized Approach Based on CNN and GA (2020)

Sentiment analysis is a computational analysis of unstructured textual data, used to assess the person's attitude from a piece of text. Aspect-based sentimental analysis defines the relationship among opinion targets of a document and the polarity values corresponding to them. Since aspects are often implicit, it is an extremely challenging task to spot them and calculate their respective polarity. In recent years, several methods, strategies and improvements have been suggested to address these problems at various levels, including corpus or lexicon-based approaches, term frequency and reverse document frequency approaches. These strategies are quite effective when aspects are correlated with predefined groups and may struggle when low-frequency aspects are involved. In terms of accuracy, heuristic approaches are stronger than frequency and lexicon based approaches, however, they consume time due to different combinations of features. This article presents an effective method to analyze the sentiments by integrating three operations: (a) Mining semantic features (b) Transformation of extracted corpus using Word2vec (c) Implementation of CNN for the mining of opinion. The hyperparameters of CNN are tuned with Genetic Algorithm (GA). Experimental results revealed that the proposed technique gave better results than the state-of-the-art techniques with 95.5% accuracy rate, 94.3% precision rate, 91.1% recall and 96.0% f-measure rate.
Photomodulation of bacterial growth and biofilm formation using carbohydrate-based surfactants (2016)

Naturally occurring and synthetic carbohydrate amphiphiles have emerged as a promising class of antimicrobial and antiadhesive agents that act through a number of dynamic and often poorly understood mechanisms. In this paper, we provide the first report on the application of azobenzene <i>trans</i>-<i>cis</i> photoisomerization for effecting spatial and temporal control over bacterial growth and biofilm formation using carbohydrate-based surfactants. Photocontrollable surface tension studies and small angle neutron scattering (SANS) revealed the diverse geometries and dimensions of self-assemblies (micelles) made possible through variation of the head group and UV-visible light irradiation. Using these light-addressable amphiphiles, we demonstrate optical control over the antibacterial activity and formation of biofilms against multi-drug resistant (MDR) <i>Pseudomonas aeruginosa</i>, methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and Gram-negative <i>Escherichia coli</i>. To probe the mechanism of bioactivity further, we evaluated the impact of <i>trans</i>-<i>cis</i> photoisomerization in these surfactants on bacterial motility and revealed photomodulated enhancement in swarming motility in <i>P. aeruginosa</i>. These light-responsive amphiphiles should attract significant interest as a new class of antibacterial agents and as investigational tools for probing the complex mechanisms underpinning bacterial adhesion and biofilm formation.
Protection of Cap-dependent Protein Synthesisin Vivo and in Vitro with an eIF4G-1 Variant Highly Resistant to Cleavage by Coxsackievirus 2A Protease (2003)

The shutoff of host protein synthesis by certain picornaviruses is mediated, at least in part, by proteolytic cleavage of eIF4G-1. Previously, we developed a cleavage site variant of eIF4G-1, termed eIF4G-1(SM), that was 100-fold more resistant to in vitro cleavage by Coxsackievirus 2A protease (2A(Pro)) than wild-type eIF4G-1 (eIF4G-1(WT)), but it was still digested at high protease concentrations. Here we identified a secondary cleavage site upstream of the primary site. We changed Gly at the P1'-position of the secondary site to Ala to produce eIF4G-1(DM). eIF4G-1(DM) was 1,000-10,000-fold more resistant to cleavage in vitro than eIF4G-1(WT). Full functional activity of eIF4G-1(DM) was demonstrated in vitro by its ability to restore cap-dependent translation to a 2A(Pro)-pretreated rabbit reticulocyte system. An isoform containing the binding site for poly(A)-binding protein, eIF4G-1e(DM), was more active in this assay than an isoform lacking it, eIF4G-1a(DM), but only with polyadenylated mRNA. Functional activity was also demonstrated in vivo with stably transfected HeLa cells expressing eIF4G-1(DM) from a tetracycline-regulated promoter. Cap-dependent green fluorescent protein synthesis was drastically inhibited by 2A(Pro) expression, but synthesis was almost fully restored by induction of either eIF4G-1a(DM) or eIF4G-1e(DM). By contrast, encephalomyocarditis virus internal ribosome entry site-dependent green fluorescent protein synthesis was stimulated by 2A(Pro); stimulation was suppressed by eIF4G-1e(DM) but not eIF4G-1a(DM).
Noise cancellation by a whole-cortex SQUID MEG system (1995)

We report on the noise cancellation performance of several whole-cortex MEG systems operated under diverse noise conditions, ranging from unshielded environments to moderately shielded rooms. The noise cancellation is performed by means of spatial filtering using high order gradiometers (2nd or 3rd), which can be formed optionally either by SQUID electronics firmware or by software. The spatial dependence of the gradiometer responses was measured in an unshielded environment and compared with simulations to yield an estimate of the system common mode magnitudes relative to field, 1st, and 2nd gradients. High order gradiometers were also formed when the system was operated in moderately shielded rooms. The combination of the spatial filtering and room shielding resulted in very high combined noise rejections approaching that of high quality shielded rooms. Examples of noise cancellation under various conditions are shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Yersinia enterocolitica type 3 secretion system (T3SS) as toolbox for studying the cell biological effects of bacterial Rho GTPase modulating T3SS effector proteins (2011)

The bacterial effector proteins IpgB(1) and IpgB(2) of Shigella and Map of Escherichia coli activate the Rho GTPases Rac1, RhoA and Cdc42, respectively, whereas YopE and YopT of Yersinia inhibit these Rho family GTPases. We established a Yersinia toolbox which allows to study the cellular effects of these effectors in different combinations in the context of Yersinia type 3 secretion system (Ysc)-T3SS-mediated injection into HeLa cells. For this purpose hybrid proteins were constructed by fusion of YopE with the effector protein of interest. As expected, injected hybrid proteins induced membrane ruffles and Yersinia uptake for IpgB(1) , stress fibres for IpgB(2) and microspikes for Map. By co-infection experiments we could demonstrate (i) IpgB(2) -mediated and ROCK-dependent inhibition of IpgB(1) -mediated Rac1 effects, (ii) YopT-mediated suppression of IpgB(1) -induced Yersinia invasion and (iii) failure of YopE-mediated suppression of IpgB(1) -induced Yersinia invasion, presumably due to preferential inhibition of RhoG by YopE GAP function. By infecting polarized MDCK cells we could demonstrate that Map or IpgB(1) but not IpgB(2) affects cell monolayer integrity. In summary, the Yersinia toolbox is suitable to study cellular effects of effector proteins of diverse bacterial species separately or in combination in the context of bacterial T3SS-mediated injection.
DNA Variants of BAT-25 in Japanese, a Locus Frequently Used for Analysis of Microsatellite Instability (2001)

BAT-25 is a DNA marker, intragenic to the c-kit protooncogene, assigned to 4q12, containing a polythymine tract, mostly repeats of 25 poly(T) (T25). The BAT-25 locus is frequently used in the analysis of microsatellite instability (MSI) in cancer tissues. The number of poly(T) repeats at BAT-25 is reported to be quasi-monomorphic and this property permits the easy identification of the MSI status. We report DNA variants of BAT-25, in one patient with hereditary nonpolyposis colorectal cancer presenting T21 and T25 alleles and another carrying T18 and T25 alleles in the analysis of 100 normal Japanese donors. Observed allelic frequencies were 0.5% for both T21 and T18 alleles. So far, DNA variants of BAT-25 locus have been reported in African Americans with relatively high frequencies, but not in Japanese.
Epigenetic Control of Autophagy in Cancer Cells: A Key Process for Cancer-Related Phenotypes (2019)

Although autophagy is a well-known and extensively described cell pathway, numerous studies have been recently interested in studying the importance of its regulation at different molecular levels, including the translational and post-translational levels. Therefore, this review focuses on the links between autophagy and epigenetics in cancer and summarizes the. following: (i) how <i>ATG</i> genes are regulated by epigenetics, including DNA methylation and post-translational histone modifications; (ii) how epidrugs are able to modulate autophagy in cancer and to alter cancer-related phenotypes (proliferation, migration, invasion, tumorigenesis, etc.) and; (iii) how epigenetic enzymes can also regulate autophagy at the protein level. One noteable observation was that researchers most often reported conclusions about the regulation of the autophagy flux, following the use of epidrugs, based only on the analysis of LC3B-II form in treated cells. However, it is now widely accepted that an increase in LC3B-II form could be the consequence of an induction of the autophagy flux, as well as a block in the autophagosome-lysosome fusion. Therefore, in our review, all the published results describing a link between epidrugs and autophagy were systematically reanalyzed to determine whether autophagy flux was indeed increased, or inhibited, following the use of these potentially new interesting treatments targeting the autophagy process. Altogether, these recent data strongly support the idea that the determination of autophagy status could be crucial for future anticancer therapies. Indeed, the use of a combination of epidrugs and autophagy inhibitors could be beneficial for some cancer patients, whereas, in other cases, an increase of autophagy, which is frequently observed following the use of epidrugs, could lead to increased autophagy cell death.
EEG hyper-connectivity in high-risk infants is associated with later autism (2014)

The results suggest that early hyper-connectivity in the alpha frequency range is an important feature of the ASD neurophysiological phenotype.