gebhart/patrepeval huggingface dataset:
Hill-based dissimilarity indices and null models for analysis of microbial community assembly (2020)

Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package ( https://github.com/omvatten/qdiv ). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines. Video Abstract.
Atomic and Electronic Structure of Solids (2003)

This text is a modern treatment of the theory of solids. The core of the book deals with the physics of electron and phonon states in crystals and how they determine the structure and properties of the solid. The discussion uses density functional theory as a starting point and covers electronic and optical phenomena, magnetism and superconductivity. There is also an extensive treatment of defects in solids, including point defects, dislocations, surfaces and interfaces. A number of modern topics where the theory of solids applies are also explored, including quasicrystals, amorphous solids, polymers, metal and semiconductor clusters, carbon nanotubes and biological macromolecules. Numerous examples are presented in detail and each chapter is accompanied by problems and suggested further readings. An extensive set of appendices provides all the necessary background for deriving all the results discussed in the main body of the text.
Ciliary Neurotrophic Factor Receptor Regulation of Adult Forebrain Neurogenesis (2013)

Appropriately targeted manipulation of endogenous neural stem progenitor (NSP) cells may contribute to therapies for trauma, stroke, and neurodegenerative disease. A prerequisite to such therapies is a better understanding of the mechanisms regulating adult NSP cells in vivo. Indirect data suggest that endogenous ciliary neurotrophic factor (CNTF) receptor signaling may inhibit neuronal differentiation of NSP cells. We challenged subventricular zone (SVZ) cells in vivo with low concentrations of CNTF to anatomically characterize cells containing functional CNTF receptors. We found that type B "stem" cells are highly responsive, whereas type C "transit-amplifying" cells and type A neuroblasts are remarkably unresponsive, as are GFAP(+) astrocytes found outside the SVZ. CNTF was identified in a subset of type B cells that label with acute BrdU administration. Disruption of in vivo CNTF receptor signaling in SVZ NSP cells, with a "floxed" CNTF receptor α (CNTFRα) mouse line and a gene construct driving Cre recombinase (Cre) expression in NSP cells, led to increases in SVZ-associated neuroblasts and new olfactory bulb neurons, as well as a neuron subtype-specific, adult-onset increase in olfactory bulb neuron populations. Adult-onset receptor disruption in SVZ NSP cells with a recombinant adeno-associated virus (AAV-Cre) also led to increased neurogenesis. However, the maintenance of type B cell populations was apparently unaffected by the receptor disruption. Together, the data suggest that endogenous CNTF receptor signaling in type B stem cells inhibits adult neurogenesis, and further suggest that the regulation may occur in a neuron subtype-specific manner.
Resource Allocation for V2X Communications: A Large Deviation Theory Perspective (2019)

In vehicular communications, one of the key requirements of the vehicle-to-vehicle (V2V) links is to transmit a given amount of data successfully during a given time period. To this end, this letter investigates a spectrum and power allocation problem in vehicular networks to maximize the sum ergodic capacity of the vehicle-to-network (V2N) links subject to the V2V links’ data amount violation probability. By using the large deviation theory, we express the data amount outage probability in a tractable form and derive the optimal power allocation for each possible spectrum reusing pair consisting of one V2N link and one V2V link. Then, the optimal spectrum reusing pattern is obtained by addressing a bipartite matching issue. Finally, the effectiveness of our proposal is validated by simulation results.
Channel coding: The road to channel capacity (2007)

Starting from Shannon's celebrated 1948 channel coding theorem, we trace the evolution of channel coding from Hamming codes to capacity-approaching codes. We focus on the contributions that have led to the most significant improvements in performance versus complexity for practical applications, particularly on the additive white Gaussian noise channel. We discuss algebraic block codes, and why they did not prove to be the way to get to the Shannon limit. We trace the antecedents of today's capacity-approaching codes: convolutional codes, concatenated codes, and other probabilistic coding schemes. Finally, we sketch some of the practical applications of these codes.
Quality of service policy control in virtual private networks (2004)

This paper studies the QoS of VPN in an environment where the public network prices connection-oriented services based on source, destination and grade of service, and advertises these prices to its VPN customers (users). As different QoS technologies can produce different QoS, there are according different traffic classification rules and priority rules. The internet service provider (ISP) may need to build complex mechanisms separately for each node. In order to reduce the burden of network configuration, we need to design policy control technologies. We considers mainly directory server, policy server, policy manager and policy enforcers. Policy decision point (PDP) decide its control according to policy rules. In network, policy enforce point (PEP) decide its network controlled unit. For InterServ and DiffServ, we will adopt different policy control methods as following: (1) In InterServ, traffic uses resource reservation protocol (RSVP) to guarantee the network resource. (2) In DiffServ, policy server controls the DiffServ code points and per hop behavior (PHB), its PDP distributes information to each network node. Policy server will function as following: information searching; decision mechanism; decision delivering; auto-configuration. In order to prove the effectiveness of QoS policy control, we make the corrective simulation.
Uncommon Presentations of Plasma Cell Dyscrasias (2017)

Plasma cell dyscrasias encompass a spectrum of malignant and premalignant conditions ranging from monoclonal gammopathy of undetermined significant to symptomatic multiple myeloma. The more common presentation of these disorders is outside the scope of this chapter. Rather, this chapter reviews uncommon presentations of multiple myeloma (IgD, IgE, IgM, or nonsecretory) as well as rare plasma cell dyscrasias (including plasma cell leukemia, POEMS (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes), primary systemic amyloidosis, solitary plasmacytomas, and heavy chain diseases). Waldenström macroglobulinemia, a subtype of lymphoplasmacytic lymphoma, will also be discussed here.
Determination of the optimal electrical bandwidth in CCD- and CMOS-based image detector applications (2004)

Limiting the electrical frequency response of the output video prior to analog-to-digital conversion is a common technique used to maximize the signal to noise ratio in imaging systems employing CCD and CMOS based solid-state detectors. Bandwidth limiting effectively reduces the magnitude of the stochastic noise in the video signal prior to digitization; but this filtering action can also change the information content in the video stream if it is applied too liberally. Various "rules of thumb" exist in the detector community for setting the bandwidth in video processing electronics. However, it will be shown that significant signal errors can be induced in many applications if such general design practices are followed implicitly. This paper addresses the general question of how to optimize bandwidth limiting in systems employing either CCD or CMOS based detectors. Induced errors in pixel signal and spatial frequency response (MTF) are analyzed as a function of bandwidth limiting for both CCD and CMOS based detectors and recommended bandwidth values are presented for systems utilizing 8 through 18 bit analog-to-digital converters.
Modelling dynamic and post-dynamic recrystallization of Zy-4 during and after hot extrusion (2008)

A study of the microstructural evolution of Zircaloy-4 (Zy-4) during hot extrusion has been performed on a small scale device mounted on a standard MTS machine. Before extrusion the billets present a Wind-manstÃ¤tten lamellar microstructure. Additional data have been obtained by hot torsion tests. After hot deformation some samples have been heat treated in various conditions. Thus the fragmentated volume fraction has been quantified with optical microscopy for various strain, strain rate and temperature histories, focusing on post dynamic effects (activation and kinetics of grain growth after deformation). For describing the microstructural evolution, the model separates dynamic and post dynamic effects. The dynamic part uses a Gourdet-Montheillet approach to describe the fragmentation. The growth is described by an explicit differential Avrami approach which can model the non isothermal evolution during cooling after extrusion. The first calculations with this model provide a good prediction of the recrystallized volume fraction for several thermal and mechanical conditions. Â© 2008 Verlag Stahleisen GmbH, DÃ¼sseldorf.
Use of dielectric spectroscopy for evidencing subphases in an antiferroelectric liquid crystal (2014)

The analysis of an orthoconic antiferroelectric liquid-crystalline mixture, using dielectric spectroscopy, has revealed a plurality of ferroelectric smectic C* subphases. A great variety of relaxation responses that could indicate the presence of different SmC* subphases has been observed with the differential scanning calorimetry (DSC) technique in partial agreement with other techniques as DSC and optical microscopy. They represent smectic intermediate variants between the ferroelectric phase and the antiferroelectric one, whose study is still open and is collecting a lot of interest in academic field. The results obtained by dielectric spectroscopy were compared with other techniques as differential scanning calorimetry and polarized optical microscopy. The results demonstrate the possibility of using dielectric spectroscopy to highlight subphases that cannot be observed with conventional experimental techniques.
Gelsolin overexpression enhances neurite outgrowth in PC12 cells (2001)

The rational design of therapies for treating nerve injuries requires an understanding of the mechanisms underlying neurite extension. Neurite motility is driven by actin polymerization; however, the mechanisms are not clearly understood. One actin accessory protein, gelsolin, is involved with remodeling the cytoskeleton, although its role in cell motility is unclear. We report a two-fold upregulation of gelsolin upon differentiation with nerve growth factor. Cells that were genetically modified to overexpress gelsolin have longer neurites and a greater neurite motility rate compared to controls. These data suggest that gelsolin plays an important role in neurite outgrowth.
Smart Grid Dispatching Strategy Considering the Difference of Electric Vehicle Demand (2020)

Plug-in electric vehicle (PEV) has developed rapidly in recent years. Considering the different requirements of PEV connected to the grid, a smart grid scheduling strategy considering the difference of PEV demand is proposed. According to the demand difference, PEV is divided into disordered charge PEV, schedulable charge PEV and schedulable charge and discharge PEV. After considering the difference of high and low power regulation, the schedulable PEV is divided into high power schedulable PEV and low power schedulable PEV. Finally, a multi-objective optimal dispatching model is constructed, which minimizes the operating cost of smart grid and the minimum cost paid by electric vehicles. The results of numerical examples show that reasonable scheduling of PEV can effectively improve the renewable energy consumption capacity, reduce the operating cost of smart grid and pay fees paid by PEV owners in the case of considering the different needs of PEV.
ΒΙΟΜΗΧΑΝΙΚΗ ΟΡΓΑΝΙΚΗ ΧΗΜΕΙΑ: Εισαγωγή (2015)

ΒΙΟΜΗΧΑΝΙΚΗ ΟΡΓΑΝΙΚΗ ΧΗΜEΙΑ [ΑΡΙΣΤΟΤEΛEΙΟ ΠΑΝEΠΙΣΤΗΜΙΟ ΘEΣ/ΝΙΚΗΣ, ΣΧΟΛΗ ΘEΤΙΚΩΝ EΠΙΣΤΗΜΩΝ, ΤΜΗΜΑ ΧΗΜEΙΑΣ]
Cobalt-Catalyzed Csp3 −Csp3 Homocoupling (2016)

International audience
Vocalization Responses After Intrathecal Administration of Ionotropic Glutamate Receptor Agonists in Rats (2002)

Vocalization responses evoked by spinal administration of ionotropic glutamate receptor agonists can be used for experimental analgesic studies. However, pathological pain models did not substantially alter vocalization responses, possibly indicating that this test is not suitable for studying the role of spinal excitatory amino acids in central sensitization.
Neurological manifestations in HTLV-1 patients with overactive bladder syndrome. A precursor of HAM/TSP? (2011)

At least 20 million people are infected with HTLV-I virus in the world, and 3 to 5 % develop the classical neurological or hematological manifestations of myelopathy (HAM/TSP) or T-cell leukemia (ATLL). HTLV-I-infected patients with overactive bladder syndrome may represent 37%. We studied 102 HTLV-1 positive individuals without HAM/TSP divided into two groups according to the presence or absence of overactive bladder (OB) syndrome. Individuals with OB were more commonly female (84.3% vs. 60.8% of asymptomatics, P = 0.01), but the mean age in the two groups was similar (46.4 ± 1.9 vs. 42.3 ± 1.7 years, respectively; P = 0.11). The prevalence of neurological complaints was higher in OB group, especially hand or foot numbness and arm or leg weakness. There was no difference between the groups in neurological strength and reflexes. Weakness remained strongly associated with OB in multivariate logistic regression analysis adjusting for sex and age (adjusted odds ratio and 95% CI 3.59(1.45-8.88) in arms and 6.68(2.63-16.93) in legs). In summary, we have characterized a subgroup of HTLV-1 infected patients based on urinary complaints who have more frequent neurological symptoms compared to those without OB. Longitudinal studies are needed to determine if HTLV-1 associated OB is a precursor of HAM/TSP.
Illumination-independent high-efficiency joint transform correlator (1991)

A novel polarization-encoded two-channel joint transform correlator is described that can produce unity interference modulation, independent of the illumination of the target and the reference.
Analysis and update of the human solute carrier (SLC) gene superfamily (2009)

The solute-carrier gene (SLC) superfamily encodes membrane-bound transporters. The SLC superfamily comprises 55 gene families having at least 362 putatively functional protein-coding genes. The gene products include passive transporters, symporters and antiporters, located in all cellular and organelle membranes, except, perhaps, the nuclear membrane. Transport substrates include amino acids and oligopeptides, glucose and other sugars, inorganic cations and anions (H(+), HCO(3)(-), Cl(-), Na(+), K(+), Ca(2+), Mg(2+), PO(4)(3-), HPO(4)(2-), H(2)PO(4)(-), SO(4)(2-), C(2)O(4)(2-), OH(-), CO(3)(2-)), bile salts, carboxylate and other organic anions, acetyl coenzyme A, essential metals, biogenic amines, neurotransmitters, vitamins, fatty acids and lipids, nucleosides, ammonium, choline, thyroid hormone and urea. Contrary to gene nomenclature commonly assigned on the basis of evolutionary divergence (http://www.genenames.org/), the SLC gene superfamily has been named based largely on transporter function by proteins having multiple transmembrane domains. Whereas all the transporters exist for endogenous substrates, it is likely that drugs, non-essential metals and many other environmental toxicants are able to 'hitch-hike' on one or another of these transporters, thereby enabling these moieties to enter (or leave) the cell. Understanding and characterising the functions of these transporters is relevant to medicine, genetics, developmental biology, pharmacology and cancer chemotherapy.
Obesity, adipokines, and C-peptide are associated with distinct plasma phospholipid profiles in adult males, an untargeted lipidomic approach (2017)

Obesity is associated with dysregulated lipid metabolism and adipokine secretion. Our group has previously reported obesity and adipokines are associated with % total fatty acid (FA) differences in plasma phospholipids. The objective of our current study was to identify in which complex lipid species (i.e., phosphatidylcholine, sphingolipids, etc) these FA differences occur. Plasma lipidomic profiling (n = 126, >95% Caucasian, 48-65 years) was performed using chromatographic separation and high resolution tandem mass spectrometry. The responses used in the statistical analyses were body mass index (BMI), waist circumference (WC), serum adipokines, cytokines, and a glycemic marker. High-dimensional statistical analyses were performed, all models were adjusted for age and smoking, and p-values were adjusted for false discovery. In Bayesian models, the lipidomic profiles (over 1,700 lipids) accounted for >60% of the inter-individual variation of BMI, WC, and leptin in our population. Across statistical analyses, we report 51 individual plasma lipids were significantly associated with obesity. Obesity was inversely associated lysophospholipids and ether linked phosphatidylcholines. In addition, we identify several unreported lipids associated with obesity that are not present in lipid databases. Taken together, these results provide new insights into the underlying biology associated with obesity and reveal new potential pathways for therapeutic targeting.
Effect of phorbol esters on the release of growth hormone and prolactin from rat pituitary cells cultured in monolayer (1984)

The effect of phorbol diester tumour promoters on the release of growth hormone (GH) and prolactin (Prl) was studied in rat pituitary cells cultured in monolayer. 12-O-tetradecanoyl phorbol-13-acetate (TPA), the most potent phorbol ester, stimulated GH accumulation in the cultured medium in a dose-dependent manner. TPA also stimulated Prl accumulation. A time course study indicated that TPA mainly stimulates release of GH. The maximal stimulation of GH release by TPA (100 ng/ml) was 3-4-fold over control. Phorbol-12,13-dibutyrate (PDB), another tumour-promoting phorbol ester, stimulated GH release to an extent similar to that of TPA, while a biologically inactive compound, phorbol-12,13-diacetate (PDA), had no effect. TPA-stimulated GH release was not affected by the presence of indomethacin, an inhibitor of prostaglandin (PG) synthesis, indicating that PG is not involved in the process of TPA-stimulated GH release. Co++, a competitive antagonist of Ca++, at 2.0 mM completely suppressed the GH release induced by TPA, and this inhibition was partially reversed by the addition of 2.0 mM Ca++. Verapamil, a Ca++ channel blocker, reduced TPA-stimulated GH release, and trifluoperazine, an inhibitor of Ca-calmodulin formation, had a similar effect. Somatostatin (SRIF) also inhibited the GH release by TPA. These observations are compatible with the idea that Ca++ may be involved in the process of TPA-stimulated GH release. Since TPA has been reported to activate a Ca++- and phospholipid-dependent protein kinase (protein kinase C), it is possible that TPA stimulate GH release by activating the enzyme. Further studies are required to clarify this point.
Biomarker modelling of Alzheimer's disease using in vivo Braak staging (2022)

Abstract Background Gold standard diagnostic methods for AD rely on staging systems to measure disease severity, which have not yet been incorporated into the in vivo biological research framework for AD. The topographical information conferred by tau‐PET offers the potential to translate the gold standard histopathological Braak staging system to living individuals. Method Using the topographical information from [ 18 F]MK6240 tau‐PET, we applied the Braak tau staging system to 324 living individuals. We used PET‐based Braak stage to model the trajectories of amyloid‐b, phosphorylated tau in cerebrospinal fluid (pTau 181 , pTau 217 , pTau 231 , pTau 235 ) and plasma (pTau 181, pTau 231 ), neurodegeneration and cognitive symptoms. Result PET‐based Braak stages were We identified nonlinear AD biomarker trajectories corresponding to the spatial extent of tau‐PET, with modest biomarker changes detectable by Braak stage II and significant changes occurring at stages III‐IV, followed by plateaus. Early Braak stages were associated with isolated memory impairment, while Braak stages V‐VI were incompatible with normal cognition. Follow up tau‐PET scans indicated sequential progression of in vivo Braak stages over time, with progression beyond Braak stage III requiring the presence of amyloid‐beta abnormality. Conclusion Our results support PET‐based Braak staging as a framework to model the natural history of AD, as well as monitor AD severity from presymptomatic to clinical dementia phases.
[Prevalence of antiborrelia antibodies in two populations: various interpretations of the same data]. (2002)

We provided evidence that when using a different formulation of the hypothesis while using correct statistical methods identical data can be differently interpreted. Thus in the interpretation of the prevalence of antiborrelia antibody levels in healthy populations with a different risk--even if the two groups do not differs as to the frequency of positive findings, there is a significant statistical difference in their distribution.
Multiplexed single‐cell analysis of FNA allows accurate diagnosis of salivary gland tumors (2022)

Diagnosing salivary gland tumors (SGTs) through fine-needle aspiration (FNA) biopsies is challenging due to the overlapping cytomorphologic features between benign and malignant tumors. The authors developed an innovative, multiplexed cycling technology for the rapid analyses of single cells obtained from FNA that can facilitate the molecular analyses and diagnosis of SGTs. Antibodies against 29 protein markers associated with 7 SGT subtypes were validated and chemically modified via custom linker-bio-orthogonal probes (FAST). Single-cell homogenates and FNA samples were profiled by FAST cyclic imaging and computational analysis. A prediction model was generated using a training set of 151,926 cells from primary SGTs (N = 26) and validated on a separate cohort (N = 30). Companion biomarker testing, such as neurotrophic tyrosine receptor kinase (NTRK), was also assessed with the FAST technology. The FAST molecular diagnostic assay was able to distinguish between benign and malignant SGTs with an accuracy of 0.86 for single-cell homogenate samples and 0.88 for FNA samples. Profiling of multiple markers as compared to a single marker increased the diagnostic accuracy (0.82 as compared to 0.65-0.74, respectively), independent of the cell number sampled. NTRK expression was also assessed by the FAST assay, highlighting the potential therapeutic application of this technology. Application of the novel multiplexed single-cell technology facilitates rapid biomarker testing from FNA samples at low cost. The customizable and modular FAST-FNA approach has relevance to multiple pathologies and organ systems where cytologic samples are often scarce and/or indeterminate resulting in improved diagnostic workflows and timely therapeutic clinical decision-making.