gebhart/patrepeval huggingface dataset:
Identification of a cDNA Encoding Tubulointerstitial Nephritis Antigen (1995)

Tubulointerstitial nephritis antigen (TIN-ag) is a 58-kDa basement membrane glycoprotein that is recognized by human autoantibodies in certain forms of tubulointerstitial nephritis. To further characterize this macromolecule and isolate cDNAs encoding TIN-ag, amino acid sequences from tryptic peptides were used to design and synthesize primers in order to amplify a probe for screening a rabbit kidney cortex cDNA library. A cDNA encoding TIN-ag was cloned and sequenced. The predicted amino acid sequence deduced from this cDNA includes the chemically determined sequences of peptides derived from TIN-ag, supporting its authenticity. The predicted amino acid sequence also shows that the carboxyl-terminal region of the molecule exhibits a 30% homology with human preprocathepsin B, a member of the cysteine proteinase family of proteins. A domain in the amino-terminal region of TIN-ag contains an epidermal growth factor-like motif that shares homology with laminin A and S chains, alpha 1 chain of type I collagen, von Willebrand's factor, and mucin, suggesting structural and perhaps functional similarities among these molecules. Immunoprecipitation of in vitro generated recombinant protein using a TIN-ag-specific monoclonal antibody (A8), confirms the identity of the isolated TIN-ag cDNA. In this report the cDNA and predicted amino acid sequences of TIN-ag are presented. Knowledge of the primary structure of TIN-ag will facilitate our understanding of the molecular structure of this novel basement membrane component and may provide clues toward understanding its functional role.
Big Data Based Logistics Data Mining Platform: Architecture and Implementation (2014)

With the development of intelligent logistics, enormous amount of logistics data are be-coming one of the sources of big data. Building the logistics information platform with big data mining and analysis capabilities to make full use of the huge logistics data is the inexorable trend for intelligent logistics. This paper studied the characteristics of the logistics big data, then, a big data based logistics data mining platform is designed and implemented by utilizing big data processing and storage techniques. The architecture and functions of the platform will be described in detail. This paper also studied the mining steps and requirements for logistics data mining, which is significant for practical applications.
Data from Prevention of Colorectal Carcinogenesis by DNA-Binding Small-Molecule Curaxin CBL0137 Involves Suppression of Wnt Signaling (2023)

&lt;div&gt;Abstract&lt;p&gt;Chemoprevention is considered a valid approach to reduce the incidence of colorectal cancer, one of the most common malignancies worldwide. Here, we investigated the tumor-preventive activity of curaxin CBL0137. This compound represents a new class of nonmutagenic DNA-binding small molecules that alter chromatin stability and inhibit the function of the histone chaperone FACT. Among downstream effects of CBL0137 treatment are activation of p53 and type I interferons and inhibition of NFκB, HSF1, and MYC. In addition, our data show that in both human and mouse colorectal cancer cells &lt;i&gt;in vitro&lt;/i&gt;, CBL0137 inhibits the APC/WNT/β-catenin signaling pathway, which plays a key role in colon carcinogenesis. Using quantitative RT-PCR and microarray hybridization, we have demonstrated decreased expression of multiple components and downstream targets of the WNT pathway in colon cancer cells treated with CBL0137. At the same time, CBL0137 induced expression of WNT antagonists. Inhibition of WNT signaling activity by CBL0137 was also confirmed by luciferase reporter assay. Tumor-preventive activity of CBL0137 &lt;i&gt;in vivo&lt;/i&gt; was tested in a murine model of colorectal carcinogenesis induced by 1,2-dimethylhydrazine (DMH), which is known to involve WNT pathway dysregulation. After DMH subcutaneous treatment, mice were administered CBL0137 in drinking water. Efficacy of CBL0137 in suppressing development of colorectal cancer in this model was evidenced by reduced incidence of adenocarcinomas and adenomas in both males and females and decrease in tumor multiplicity. These data support the prospective use of CBL0137 in chemoprevention of colorectal cancer as well as of other malignances associated with activated WNT signaling.&lt;/p&gt;&lt;/div&gt;
Pathway for Large-Scale Conformational Change in Annexin V (2000)

Crystallographic studies have shown that the binding of calcium to domain III of annexin V is accompanied by a large conformational change involving surface exposure of Trp187. Here we examine this conformational transition using computer simulation. It is found that the burial of Trp187 is accompanied by a large increase in conformational strain, compensated by improved protein-protein interaction energies. A low energy pathway for the conformational change is determined using the conjugate peak refinement method [Fischer, S., and Karplus, M. (1992) Chem. Phys. Lett. 194, 252-261] with solvent effects taken into account using nonuniform charge scaling. The pathway obtained is complex, involving >300 dihedral angle transitions and the complete unwinding of one helix. Acidic residues play a key role in the conformational pathway, via a succession of direct hydrogen bonds with the indole ring of Trp187. This finding is discussed in the light of experimentally determined pH, calcium ion and mutational effects on the conformational transition.
Inhibition of dystroglycan binding to laminin disrupts the PI3K/AKT pathway and survival signaling in muscle cells (2002)

Dystroglycan is a component of the dystrophin-glycoprotein complex (DGC) in muscle and a cell surface receptor for laminin. Numerous muscular dystrophies are the result of disruption of proteins comprising the DGC, but the underlying pathogenetic mechanisms are unknown. Because apoptosis is an early feature of muscular dystrophy in vivo, and perturbation of cell-extracellular matrix associations is known to induce apoptosis, we investigated the role of dystroglycan-laminin interactions in the propagation and maintenance of cell survival signals in muscle cells. We found that disrupting the interaction between alpha-dystroglycan and the extracellular matrix protein laminin induces apoptosis in muscle cells. This increase in apoptosis is mediated in part by caspase activation and can be blocked by a caspase-3 inhibitor. We demonstrate a role for the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) pathway in muscle cell-survival signaling using a pharmacological inhibitor of PI3K. Treatment with this inhibitor resulted in decreased phosphorylation of AKT and its downstream effector glycogen synthase kinase (GSK)-3beta and induced apoptosis in muscle cell cultures. Disruption of dystroglycan-laminin interactions resulted in decreased phosphorylation of AKT and GSK-3beta. Furthermore, activation of AKT prior to the disruption of dystroglycan-laminin protected the muscle cells from the induction of apoptosis. These results support a role for the PI3K/AKT pathway in the propagation of cell-survival signals mediated by the DGC and provide new insight into the molecular pathogenesis associated with the development of muscular dystrophies.
Stereotypical reaching movements of the octopus involve both bend propagation and arm elongation (2015)

The bend propagation involved in the stereotypical reaching movement of the octopus arm has been extensively studied. While these studies have analyzed the kinematics of bend propagation along the arm during its extension, possible length changes have been ignored. Here, the elongation profiles of the reaching movements of Octopus vulgaris were assessed using three-dimensional reconstructions. The analysis revealed that, in addition to bend propagation, arm extension movements involve elongation of the proximal part of the arm, i.e., the section from the base of the arm to the propagating bend. The elongations are quite substantial and highly variable, ranging from an average strain along the arm of -0.12 (i.e. shortening) up to 1.8 at the end of the movement (0.57 ± 0.41, n = 64 movements, four animals). Less variability was discovered in an additional set of experiments on reaching movements (0.64 ± 0.28, n = 30 movements, two animals), where target and octopus positions were kept more stationary. Visual observation and subsequent kinematic analysis suggest that the reaching movements can be broadly segregated into two groups. The first group involves bend propagation beginning at the base of the arm and propagating towards the arm tip. In the second, the bend is formed or present more distally and reaching is achieved mainly by elongation and straightening of the segment proximal to the bend. Only in the second type of movements is elongation significantly positively correlated with the distance of the bend from the target. We suggest that reaching towards a target is generated by a combination of both propagation of a bend along the arm and arm elongation. These two motor primitives may be combined to create a broad spectrum of reaching movements. The dynamical model, which recapitulates the biomechanics of the octopus muscular hydrostatic arm, suggests that achieving the observed elongation requires an extremely low ratio of longitudinal to transverse muscle force (<0.0016 for an average strain along the arm of around 0.5). This was not observed and moreover such extremely low value does not seem to be physiologically possible. Hence the assumptions made in applying the dynamic model to behaviors such as static arm stiffening that leads to arm extension through bend propagation and the patterns of activation used to simulate such behaviors should be modified to account for movements combining bend propagation and arm elongation.
Na‐Ion Batteries: A General Metal‐Organic Framework (MOF)‐Derived Selenidation Strategy for In Situ Carbon‐Encapsulated Metal Selenides as High‐Rate Anodes for Na‐Ion Batteries (Adv. Funct. Mater. 16/2018) (2018)

Jun Liu, Renzong Hu, and their co-workers report a general and facile metal-organic framework (MOF)-derived selenidation strategy for carbon-encapsulated metal selenide electrodes with multiscale, multidimensional, and hierarchical architectures in article number 1707573. Due to the novel and unique architecture design, these nanohybrid electrodes display ultrastable cycling performance as well as excellent rate capability for Na-ion storage.
Circadian clock and cancer therapy: an unexpected journey (2014)

Chronotherapy of cancer is one of the oldest examples of the clinical application of biological rhythms. Growing understanding of the importance of biological timing in physiology and pathophysiology of many diseases including cancer reforms our views on the role of biological clocks in cancer and cancer treatment. In the present issue the current progress in circadian clock-dependent mechanisms of cancer, polymorphism and mutations of clock gene in cancer, cancer-associated clock disruptions, and novel chronotherapeutic approaches are discussed.
Coordinate adaptations of skeletal muscle and kidney to maintain extracellular [K+] during K+-deficient diet (2020)

Extracellular fluid (ECF) potassium concentration ([K<sup>+</sup>]) is maintained by adaptations of kidney and skeletal muscle, responses heretofore studied separately. We aimed to determine how these organ systems work in concert to preserve ECF [K<sup>+</sup>] in male C57BL/6J mice fed a K<sup>+</sup>-deficient diet (0K) versus 1% K<sup>+</sup> diet (1K) for 10 days (<i>n</i> = 5-6/group). During 0K feeding, plasma [K<sup>+</sup>] fell from 4.5 to 2 mM; hindlimb muscle (gastrocnemius and soleus) lost 28 mM K<sup>+</sup> (from 115 ± 2 to 87 ± 2 mM) and gained 27 mM Na<sup>+</sup> (from 27 ± 0.4 to 54 ± 2 mM). Doubling of muscle tissue [Na<sup>+</sup>] was not associated with inflammation, cytokine production or hypertension as reported by others. Muscle transporter adaptations in 0K- versus 1K-fed mice, assessed by immunoblot, included decreased sodium pump α2-β2 subunits, decreased K<sup>+</sup>-Cl<sup>-</sup> cotransporter isoform 3, and increased phosphorylated (p) Na<sup>+</sup>,K<sup>+</sup>,2Cl<sup>-</sup> cotransporter isoform 1 (NKCC1p), Ste20/SPS-1-related proline-alanine rich kinase (SPAKp), and oxidative stress-responsive kinase 1 (OSR1p) consistent with intracellular fluid (ICF) K<sup>+</sup> loss and Na<sup>+</sup> gain. Renal transporters' adaptations, effecting a 98% reduction in K<sup>+</sup> excretion, included two- to threefold increased phosphorylated Na<sup>+</sup>-Cl<sup>-</sup> cotransporter (NCCp), SPAKp, and OSR1p abundance, limiting Na<sup>+</sup> delivery to epithelial Na<sup>+</sup> channels where Na<sup>+</sup> reabsorption drives K<sup>+</sup> secretion; and renal K sensor Kir 4.1 abundance fell 25%. Mass balance estimations indicate that over 10 days of 0K feeding, mice lose ~48 μmol K<sup>+</sup> into the urine and muscle shifts ~47 μmol K<sup>+</sup> from ICF to ECF, illustrating the importance of the concerted responses during K<sup>+</sup> deficiency.
Robust tissue classification for reproducible wound assessment in telemedicine environments (2010)

In telemedicine environments, a standardized and reproducible assessment of wounds, using a simple free-handled digital camera, is an essential requirement. However, to ensure robust tissue classification, particular attention must be paid to the complete design of the color processing chain. We introduce the key steps including color correction, merging of expert labeling, and segmentation-driven classification based on support vector machines. The tool thus developed ensures stability under lighting condition, viewpoint, and camera changes, to achieve accurate and robust classification of skin tissues. Clinical tests demonstrate that such an advanced tool, which forms part of a complete 3-D and color wound assessment system, significantly improves the monitoring of the healing process. It achieves an overlap score of 79.3 against 69.1% for a single expert, after mapping on the medical reference developed from the image labeling by a college of experts.
Distribution of Taenia solium Diagnostic Glycoproteins in the Different Developmental Stages of the Parasite (2019)

<i>Taenia solium</i> is a helminth parasite that causes 2 diseases in humans: cysticercosis and taeniasis. The establishment of <i>T. solium</i> metacestodes in the central nervous system causes neurocysticercosis, while development of the adult tapeworm in the small intestine causes taeniasis. Serological diagnosis of neurocysticercosis is performed by Western blot with an enriched fraction of glycoproteins that has been extensively used for clinical diagnosis and epidemiological surveys. The lectin-bound fraction that is used for this assay contains 7 antigenic glycoproteins. These antigenic proteins are considered to be highly specific for cysticercosis when tested with heterologous parasitic diseases. However, recent studies show that people with taeniasis have cross-reactive antibodies against the neurocysticercosis diagnostic glycoproteins and vice versa. Nevertheless, it is not known if these diagnostic proteins are expressed in the adult stage of the parasite. In this paper, we describe the location of 3 of these glycoproteins in <i>T. solium</i> adults and cysticerci using polyclonal antibodies raised against a synthetic peptide based on the amino acid sequence of TS14, a recombinant protein T24H, and the native GP50. The glycoproteins' distribution was different in invaginated and evaginated cysticerci as well as in adult tapeworms. Specifically, the 3 glycoproteins studied were differentially expressed during embryogenesis. Our findings indicate that expression of the diagnostic glycoproteins is developmentally regulated; this is noteworthy since these glycoproteins are considered specific for the diagnosis of neurocysticercosis but nevertheless are present in different structures throughout the development of <i>T. solium</i>. Here we describe the glycoprotein expression and localization, which can be important in understanding their biological functions. In addition, our results help clarify the cross-reaction observed between people with neurocysticercosis and taeniasis to TS14, T24H, and GP50, which are used as diagnostic antigens for neurocysticercosis.
A ‘golden’ SNP in CmOr governs the fruit flesh color of melon (Cucumis melo) (2015)

The flesh color of Cucumis melo (melon) is genetically determined, and can be white, light green or orange, with β-carotene being the predominant pigment. We associated carotenoid accumulation in melon fruit flesh with polymorphism within CmOr, a homolog of the cauliflower BoOr gene, and identified CmOr as the previously described gf locus in melon. CmOr was found to co-segregate with fruit flesh color, and presented two haplotypes (alleles) in a broad germplasm collection, one being associated with orange flesh and the second being associated with either white or green flesh. Allelic variation of CmOr does not affect its transcription or protein level. The variation also does not affect its plastid subcellular localization. Among the identified single nucleotide polymorphisms (SNPs) between CmOr alleles in orange versus green/white-flesh fruit, a single SNP causes a change of an evolutionarily highly conserved arginine to histidine in the CmOr protein. Functional analysis of CmOr haplotypes in an Arabidopsis callus system confirmed the ability of the CmOr orange haplotype to induce β-carotene accumulation. Site-directed mutagenesis of the CmOr green/white haplotype to change the CmOR arginine to histidine triggered β-carotene accumulation. The identification of the 'golden' SNP in CmOr, which is responsible for the non-orange and orange melon fruit phenotypes, provides new tools for studying the Or mechanism of action, and suggests genome editing of the Or gene for nutritional biofortification of crops.
Phenotypes of sGC mutant mice in basic conditions, disease and shock (2009)

To evaluate the role of sGC in physiology and pathogenesis, we generated sGCα1-/- mice and sGCβH105F knock in mice. The latter have a heme-less and hence NO-resistant sGC, and are a model for the situation in oxidative stress, where the sGC loses its sensitivity to NO.

We observed that some of the phenotypic differences observed in sGCα1-/- are dependent on the genetic background while others are not. So, the gender-specific testosterone hypertension was obvious in male sGCα1-/- mice on a 129Sv background but not on a C57Bl/6 background, while the changes in relaxation of gastro-intestinal smooth muscle are identical in sGCα1-/- mice on both genetic backgrounds. Furthermore, while the presence of the sGCα2 β1 isoform is sufficient to retain NO responsiveness in a number of situations, the sGCα1β isoform seems to have exclusive roles.

sGCβ1H105F mice show a reduced viability, anatomical abnormalities, growth retardation, and hypertension. The blood pressure is no longer sensitive to NO donor compounds or L-NAME but the action of the sGC activator BAY58-2667 was preserved, confirming the thesis that BAY58-2667 preferentially activates the heme-free form of sGC, also in vivo.

The cardiovascular collapse in inflammatory shock (sepsis, anaphylaxis,...) is considered to depend on the NOS-2-sGC-cGK axis. However, except for NOS-3 dependent anaphylactic shock, which was partially inhibited in sGCα1-/- mice, various other forms of shock (LPS, TNF) were not attenuated in the absence of sGC, rather in contrast. In addition, we observed that in some situations, as much NOS-2 and NOS-2 derived NO is present as in lethal septic shock, without having hemodynamic consequences. These results imply that at least part of the protective properties of NO in shock are sGC dependent. They however also question the paradigm that the NO-sGC-cGK axis is the mediator of distributive shock. Indeed, we obtained evidence that some Reactive Oxygen Species might be an alternative candidate mediator, and might influence the NOS or sGC in shock.
Immediate Breast Reconstruction with Tissue Expansion (1987)

Between October of 1983 and June of 1985, 31 patients underwent primary breast reconstruction with tissue expansion. Tissue expansion was utilized for breast reconstruction when the remaining muscle and skin following modified radical mastectomy was insufficient to accommodate a prosthesis that matched in size and shape the opposite breast. All expanders were placed beneath an investing muscular pocket created by elevating the pectoralis major and serratus anterior. Postoperative expansion began within 1 week, and the breast was expanded to double the volume of the opposite breast. Twenty-two patients have completed their reconstruction with a mean follow-up in 7 months. There were nine complications, including five deflations and four infections. All patients have remained Baker I or Baker II. Creating ptosis to match the breast was accomplished by placing the expander below the rectus fascia and superiorly advancing this expanded tissue at the time of prosthesis placement. Primary breast reconstruction with tissue expansion following modified radical mastectomy is safe, simple, and produces a breast with excellent shape, size, texture, and patient satisfaction.
Bilayer-fish-scale ultrabroad terahertz bandpass filter (2012)

A bilayer fish-scale metamaterial is experimentally demonstrated to function as a broad bandpass filter in the terahertz regime. The measured 3 dB-bandwidth for normal incidence is 1.13 THz with a high transmittance. The measured transmission spectrum is described well by a model based on an RLC circuit and multiple reflections. The filter is relatively insensitive to incidence angles up to 45°.
A TCP/HSDPA rendszer átvitelének analitikus modellje (2008)

A HSDPA (High Speed Downlink Packet Access) nagysebessegu (akar tobb megabit masodpercenkent) csomagkapcsolt, letoltesiranyu szolgaltatast nyujt UMTS (Universal Mobile Telecommunications System) felett [6]. Hagyomanyos UMTS eseten az adatkapcsolati retegbeli protokollok – mint peldaul Radio Link Control (RLC) es Medium Access Control (MAC) – a radioshalozat-vezerloben (RNC, Radio Network Controller) vegzodnek. A radios interfeszt megvalosito protokollok az RNC-vel az Iub interfeszen kapcsolodo bazisallomasban (3. generacios mobilhalozatok eseten ez a Node B) vannak megvalositva. Nyugtazott modban (AM) az RLC felelos a hibamentes, sorrendhelyes atvitelert, amelyet az ARQ (Automatic Repeat Request – automatikus ujraadas) mechanizmussal ernek el, ami azonban noveli a masodik retegbeli korbefordulasi idot, igy TCP idotullepeshez vezethet. HSDPA eseten uj protokollreteget – a MAC-hs reteget – vezettek be a bazisallomasban (1. abra). Ennek segitsegevel a bazisallomas kepes gyorsan alkalmazkodni a radios interfesz aktualis allapotahoz modulacios es kodolasi semavaltassal, gyors utemezessel es ujraadassal. Ez utobbit a HARQ (Hybrid ARQ) mechanizmus valositja meg. Ezek a megoldasok segitik csokkenteni a masodik retegbeli korbefordulasi idot, ha az ujraadast a hibas radios interfesz feletti atvitel okozta. Habar ezzel a bazisallomas kezeli az ujraadast, az RLC retegbeli ujraadas is megmaradt a Rel’99-es megoldasokkal valo kompatibilitas, illetve a rendszeren beluli hivasatadas-vezerles megtartasa erdekeben. Az RLC ugyanakkor tovabbra is kezeli az ujraadast, ha a MAChs ujraadasok szama elert egy megengedett legnagyobb szamot, vagy ha a szallitasi retegben dobas volt. Igy HSDPA eseten is novelheti az RLC a korbefordulasi idot. Ezen megoldasok azt is eredmenyezik, hogy a TCP keptelen megallapitani es kezelni a torlodast, csak ha mar lejart a TCP idozitoje, vagy ha a csomag elerte az RLC ujraadasok legnagyobb megengedett szamat is es azt az RLC eldobta.