gebhart/patrepeval huggingface dataset:
Point process models for weather radar images (2002)

A framework for analysing weather radar (DBz) images as spatial point processes is presented. Weather radar images are modelled for the purpose of predicting their evolution in time and thereby providing a basis for short-period precipitation forecasts. An observed image sequence is modelled as a set of individual rain cells that are the outcome of a marked 2+1D spatial point process. To each point giving the place and time of maturation of a rain cell is assigned a vector of possibly time-varying features such as intensity, duration, extent, shape and velocity. The point process is a doubly stochastic spatial point process with a clustering mechanism determined by the mesoscale situation. Also determined by the mesoscale situation are prior distributions for the elements of the feature vector. A scheme for fitting this type of model to an observed sequence of weather radar images is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Endocrinology of Menopausal Transition and Its Brain Implications (2005)

The central nervous system is one of the main target tissues for sex steroid hormones, which act on both through genomic mechanisms, modulating synthesis, release, and metabolism of many neuropeptides and neurotransmitters, and through non-genomic mechanisms, influencing electrical excitability, synaptic function, morphological features, and neuron-glia interactions. During the climacteric period, sex steroid deficiency causes many neuroendocrine changes. At the hypothalamic level, estrogen withdrawal gives rise to vasomotor symptoms, to eating behavior disorders, and altered blood pressure control. On the other hand, at the limbic level, the changes in serotoninergic, noradrenergic, and opioidergic tones contribute to the modifications in mood, behavior, and nociception. Hormone replacement therapy (HRT) positively affects climateric depression throughout a direct effect on neural activity and on the modulation of adrenergic and serotoninergic tones and may modulate the decrease in cognitive efficiency observed in climaterium. The identification of the brain as a de novo source of neurosteroids, suggests that the modifications in mood and cognitive performances occurring in postmenopausal women may also be related to a change in the levels of neurosteroids. These findings open new perspectives in the study of the effects of sex steroids on the central nervous system and on the possible use of alternative and/or auxiliary HRT.
Synthesis and photochromic behavior of some azo-polysiloxanes modified with nucleobases or donor-acceptor groups (2007)

Abstract This paper presents the syntheses, characterization and photochromic behavior of some new azo-polysiloxanes modified with uracil, cytosine or nitro-phenolic groups. Taking into consideration the possibility of generating H-bonds or donor/acceptor interactions, this class of materials present a potential applicability in the immobilization of biomolecules and their nano-manipulations. Also, such compounds are capable of producing a fluid phase, with directional flowing capacity. For all these polymers, the molecular modeling simulations have shown disordered structures, which would generate amorphous phases, a very important aspect for molecules’ nano-manipulation. The photochromic behavior in the presence of UV irradiation was also evaluated.
Design, synthesis and antimicrobial activity of usnic acid derivatives (2018)

Usnic acid, a dibenzofuran, was originally isolated from lichens producing secondary metabolites, and is well known as an antibiotic, but is also endowed with several other interesting properties. Thus, the goal of this paper is the design of new usnic acid derivatives and evaluation of their antimicrobial activity. All newly synthesized compounds possess good antibacterial activity with MIC ranging from 1.02-50.93 × 10<sup>-2</sup> mmol mL<sup>-1</sup> and MBC from 2.05-70.57 × 10<sup>-2</sup> mmol mL<sup>-1</sup>. The most sensitive bacterial species was <i>Staphylococcus aureus</i>, while <i>Pseudomonas aeruginosa</i> and <i>Escherichia coli</i> were the most resistant among the ATCC strains, and MRSA was the most resistant among all tested bacteria (ATCC and clinical isolates). Their antifungal activity was very strong (MIC = 0.35-7.53 × 10<sup>-2</sup> mmol mL<sup>-1</sup> and MFC = 0.70-15.05 × 10<sup>-2</sup> mmol mL<sup>-1</sup>) - better than those of reference compounds and usnic acid itself. The most sensitive fungal species was <i>Trichoderma viride</i>, while <i>Penicillium versicolor</i> var. <i>cyclopium</i> appeared to be the most resistant. It should be mentioned that in general most of the compounds showed weaker antibacterial activity, but better antifungal properties than usnic acid itself. The results allow us to conclude that the title compounds are good lead compounds for novel more active antibacterial drugs. On the other hand, these compounds are very promising as antifungals.
Common complications and mechanisms of urinary system after hematopoietic stem cell transplantation in children (2017)

Hematopoietic stem cell transplantation(HSCT)is an important treatment of various hematological diseases, and urinary system injury is one of the common complications after HSCT, including acute renal damage, chronic kidney disease, nephrotic syndrome after transplantation, transplantation associated thrombotic microangiopathy, urinary tract infection, hemorrhagic cystitis, etc.The etiology includes three aspects: prerenal, renal and postrenal.Various factors have interactions with each other.The clinical manifestations, treatment and prognosis are different due to the disease types and severity.Renal biopsy is of great significance for the etiological analysis, therapeutic guide and prognostic vaule.This article reviews the common complications and mechanisms of urinary system after HSCT in children.


Key words: 
National Natural Science Foundation of China(81370787); The Jiangsu Province Clinical Medical Science and Technology Commission(SBL2014030237).
Involvement of apoptosis-related gene Survivin, bcl-2 and bax in the homoharringtonine-induced apoptosis of myelodysplastic syndrome cell line(MUTZ-1) (2003)

Objective To investigate the expression of apoptosis related genes, Survivin, bcl 2 and bax in apoptosis of MDS cell line MUTZ 1, and possible mechanisms of homoharringtonine (HHT) in the treatment of myelodysplastic syndrome (MDS). Methods The apoptosis of MDS RAEB cell line MUTZ 1 was observed by transmission electron microscope. Cell apoptosis and cell cycle shift were also investigated by flow cytometry (FCM).The expression of Survivin, bcl 2 and bax was detected by retrotranscriptase polymerase chain reaction (RT PCR). Results Apoptotic peak on FCM and positive Annexin V FITC on cell membrane showed that HHT induced apoptosis of MUTZ 1 cell in a dose and time dependent manner. HHT significantly down regulated Survivin expression, but there were no changes on bax and bcl 2 expression. Conclusion HHT could induce apoptosis of MDS cell line(MTUZ 1) and Survivin might play an important role in MDS.
Cortical thinning is associated with disease stages and dementia in Parkinson's disease (2013)

We conclude that measuring cortical thickness can be useful in assessing disease stage and cognitive impairment in patients with PD. In addition, cortical thickness may be useful in identifying dementia in PD.
Classification of tumor microenvironment immune types based on immune response-associated gene expression (2018)

In 2014, the Shizuoka Cancer Center launched project High‑tech Omics‑based Patient Evaluation (HOPE), which features whole exome sequencing (WES) and gene expression profiling (GEP) of fresh surgical specimens from cancer patients. With the development of clinical trials of programmed death‑1 (PD‑1)/PD‑ligand 1 (PD‑L1) blockade, PD‑L1 expression and a high tumor mutation burden become possible biomarkers that could be used to predict immune responses. In this study, based on WES and GEP data from 1,734 tumors from the HOPE project, we established a tumor microenvironment (TME) immune‑type classification consisting of 4 types to evaluate the immunological status of cancer patients and analyze immunological pathways specific for immune types. Project HOPE was conducted in accordance with the Ethical Guidelines for Human Genome and Genetic Analysis Research with the approval of the Institutional Review Board. Based on the expression level of the PD‑L1 and CD8B genes, the immunological status was divided into 4 types as follows: A, PD‑L1+CD8B+; B, PD‑L1+CD8B‑; C, PD‑L1‑CD8B‑; and D, PD‑L1‑CD8B+. Type A, with PD‑L1+ and CD8B+, exhibited an upregulation of cytotoxic T lymphocyte (CTL) killing‑associated genes, T‑cell activation genes, antigen‑presentation and dendritic cell (DC) maturation genes, and T‑cell‑attracting chemokine genes, which promoted Th1 antitumor responses. By contrast, type C, with PD‑L1‑ and CD8B‑, exhibited a low expression of T‑cell‑activating genes and an upregulation of cancer driver gene signaling, which suggested an immune‑suppressive status. With regard to hypermutator tumors, PD‑L1+ hypermutator cases exhibited a specific upregulation of the IL6 gene compared with the PD‑L1‑ cases. On the whole, our data indicate that the classification of the TME immune types may prove to be a useful tool for evaluating the immunological status and predicting antitumor responses and prognosis.
Extraction and remeshing of ellipsoidal representations from mesh data (2005)

Dense 3D polygon meshes are now a pervasive product of various modelling and scanning processes that need to be subsequently processed and structured appropriately for various applications. In this paper we address the restructuring of dense polygon meshes using their segmentation based on a number of ellipsoidal regions. We present a simple segmentation algorithm where connected components of a mesh are fit to ellipsoidal surface regions. The segmentation of a mesh into a small number of ellipsoidal elements makes for a compact geometric representation and facilitates efficient geometric queries and transformations. We also contrast and compare two polygon remeshing techniques based on the ellipsoidal surfaces and the segmentation boundaries.
A static CMOS master-slave flip-flop experiment (2002)

A variant of a classical master-slave flip-flop based on transmission gates is derived where the transmission gates are replaced by static CMOS gates. The transmission gate flip-flop and the variant are evaluated along with one flip-flop based on C/sup 2/MOS latches and another based on SR latches. All flip-flops are edge-triggered. The propagation delay, set-up time, and hold time are estimated using a 0.35 /spl mu/m process. The author also investigates how the power dissipation at the maximal clock frequency varies when the supply voltage is scaled, both when the device geometry is kept constant and when it is scaled to yield good noise margins. In comparison, the variant on master-slave flip-flop has short propagation delay, but is only average in terms of throughput and power consumption. The flip-flop realized with C/sup 2/MOS latches seems to be a better candidate for a general-purpose implementation when voltage scaling is an option.
Isolation, primary structure, and evolution of the third component of chicken complement and evidence for a new member of the <i>alpha</i>  2-macroglobulin family. (1995)

Although the third component of complement, C3, has been isolated and its primary structure determined from most living classes of vertebrate, limited information is available on its structure and function for aves, which represent a significant stage in complement evolution. In this study, we present the complete cDNA sequence of chicken C3, the cDNA sequences of the thioester region for two chicken alpha 2-macroglobulin (alpha 2M)-related proteins, a simplified method for purifying chicken C3, and an analysis of the C3 convertase and factor I-mediated cleavages in chicken C3. Using the reverse-transcriptase PCR, with degenerate oligonucleotide primers derived from two conserved C3 sequences (GCGEQN/TM, TWLTAY/FV) and liver mRNA as template, we isolated three distinct 220-bp PCR products, one with a high degree of sequence similarity to C3 and two to alpha 2M and pregnancy zone protein from other species. The complete cDNA sequence of chicken C3 was obtained by screening a chicken liver lambda gt10 library with the C3 PCR product and probes from the 5' end of the partial-length C3 clones. The obtained sequence is in complete agreement with the protein sequence of several tryptic peptides of purified chicken C3. Chicken pro-C3 consists of an 18-residue putative signal peptide, a 640-residue beta-chain (70 kDa), a 989-residue alpha-chain (111 kDa), and an RKRR linker region. It contains an internal thioester and three potential N-glycosylation sites, all in the alpha-chain. The convertase cleavage site, predicted to be Arg-Ser, was confirmed by sequencing the zymosan-bound C3 fragments generated upon complement activation. NH2-terminal sequencing of the purified C3 chains showed that 1) pro-C3 is indeed cleaved at the RKRR linker sequence to generate the mature two-chain molecule, and 2) the beta-chain of chicken C3 is blocked. The deduced amino acid sequence shows 54, 54, 54, 53, 52, 57, and 55% amino acid identities to human, mouse, rat, guinea pig, rabbit, cobra, and Xenopus C3, respectively, and an identity of 44, 31, and 33% to trout, hagfish, and lamprey C3, respectively. The identities to human C4, C5, and alpha 2M are 31, 29 and 23%, respectively. A phylogenetic tree for C3, C4, C5, and alpha 2M-related proteins was constructed based on the sequence data and is discussed.
Assessing the performance of fold recognition methods by means of a comprehensive benchmark. (1996)

Recently there has been an explosion of methods for fold recognition. These methods seek to align a protein sequence to a three-dimensional structure and measure the compatibility of the sequence to the structure. In this work, we present a benchmark to assess the performance of such methods. The benchmark consists of a set of protein sequences matched by superposition to known structures. This set covers a wide range of protein families, and includes matching proteins with insignificant sequence similarity. To demonstrate the usefulness of this benchmark, we apply it here to compare different fold-recognition methods developed through the years in our group as well as several sequence-sequence substitution matrices. The results show that "global-local" alignments are superior to either local or global alignments. The most effective sequence-sequence matching matrix is the Gonnet table. The best performance overall is obtained by a method which combines the 3D-1D profiles of Bowie et al. with a substitution matrix and takes into account residue pairwise interactions.
Preferential expression of fibronectin receptors on immature thymocytes. (1988)

Fibronectin-adherent (FNR+) thymocytes are enriched for immature (CD4-8-) and large (CD4+8+) cells, and depleted of mature (CD4-8+ and CD4+8-) and nonmature small (CD4+8+) cells. Among purified CD4-8- thymocytes, cells with the surface marker J11d and the IL-2 receptor, which can give rise to all other thymocyte subsets, showed selective attachment to fibronectin. Analysis of FNR+ thymocytes showed that such cells are greatly enriched for cells in cycle. Additionally, FNR+ cells expressed low levels of T cell receptor. These results suggest a role for the fibronectin receptor during the early, proliferative phase of thymocyte differentiation. The data suggest that loss of the fibronectin receptor is a hallmark of cells that have become committed either to functional maturation or to programmed cell death.
Towards an actor-based concurrent machine model (2009)

In this position paper we propose to extend an existing delegation-based machine model with concurrency primitives. The original machine model which is built on the concepts of objects, messages, and delegation, provides support for languages enabling multi-dimensional separation of concerns (MDSOC). We propose to extend this model with an actor-based concurrency model, allowing for both true parallelism as well as lightweight concurrency primitives such as coroutines. In order to demonstrate its expressiveness, we informally describe how three high-level languages supporting different concurrency models can be mapped onto our extended machine model. We also provide an outlook on the extended model's potential to support concurrency-related MDSOC features.
Active Range-Only beacon localization for AUV homing (2014)

This paper presents a solution to the 3D Range-Only beacon localization problem using a Sum of Gaussians (SOG) filter together with an Active Localization method, which is based on the minimization of the beacon position uncertainty, in order to ensure the problem observability and a fast convergence. The method is applied to autonomously locate a subsea panel and home to it in order to establish visual contact to later launch a visual servoing based docking task. The method is demonstrated through field experiments in a harbor environment with an Autonomous Underwater Vehicle (AUV) including Ultra-Short Baseline (USBL) ground truth information.
Preclinical Protocol for in Vivo Selection of Hematopoietic Stem Cells Corrected by Gene Therapy in Fanconi Anemia Group C (2001)

Fanconi anemia (FA) is an autosomal recessive disorder characterized by birth defects, increased incidence of malignancy, progressive bone marrow failure, and cellular hypersensitivity to DNA cross-linking agents. Bone marrow transplantation is therapeutic and therefore FA is a candidate disease for hematopoietic gene therapy. We have previously used mitomycin C (MMC) to achieve in vivo selection of wild-type hematopoietic stem cells (HSC) transplanted into FANCC knockout mice. However, clinical application of MMC in human FA gene therapy is unlikely because of its unknown toxicity profile in human FA patients. In contrast, cyclophosphamide (CPA) and gamma-irradiation (IR) are already in use with human FA patients and we therefore tested these regimens for their ability to achieve selection of genetically corrected HSCs in vivo. We found that nonmyeloablative doses of CPA or IR or combinations of CPA + IR were highly efficient at achieving in vivo selection of transplanted wild-type HSC. Furthermore, this nontoxic regimen also selected FANCC-mutant HSC corrected by ex vivo retroviral gene therapy. We suggest those nontoxic doses of CPA and/or IR could also be used to enhance gene therapy in human FA patients.
Regional intratidal gas distribution in acute lung injury and acute respiratory distress syndrome assessed by electric impedance tomography. (2010)

On-line intratidal gas distribution monitoring offers additional information on recruitability and optimal PEEP.
Stool therapy may become a preferred treatment of recurrent<i>Clostridium difficile</i>? (2013)

Fecal enemas were first reported to successfully treat life threatening enterocolitis in 1958, but fecal therapy to treat Clostridium difficile (C. difficile) infection has remained esoteric and not well investigated until recently. In the past few years, systematic reviews of case series and case reports of fecal microbiota transplant for recurrent C. difficile infection have become available and validate use of fecal transplant for C. difficile enterocolitis. Methods of fecal transplant reported in the literature include: nasogastric tube, gastroscope, duodenal tube, colonoscopy, rectal tube, and fecal enemas administered at home; no method has been shown to be superior. A recent randomized study published in New England Journal of Medicine found fecal transplant to be superior to oral vancomycin alone in treatment of recurrent C. difficile enterocolitis. The significance of this trial cannot be underestimated as it lends credibility to the idea of intentionally using microbes to combat disease, providing an alternative to the older paradigm of disease eradication through use of antimicrobials.
Phase engineering and supercompatibility of shape memory alloys (2017)

In recent years examples of unprecedented functional and structural fatigue resistance and lowered hysteresis in shape memory alloys have been achieved by combining conditions of supercompatibility between phases with suitable grain size and a favorable array of fine precipitates. We collect, review and compare these examples to elucidate the relative roles of these factors, especially in the case of the more demanding stress-induced phase transformations, and we pose key open questions. The control of these factors lends itself to systematic alloy development. Taken together, these results point to significant opportunities to discover improved shape memory alloys as well has new reversible transforming multiferroics.
Self-Assembled Monolayers of Dodecyl and Hydroxy-dodecyl Phosphates on Both Smooth and Rough Titanium and Titanium Oxide Surfaces (2002)

Dodecyl phosphate and hydroxy-terminated dodecyl phosphate are shown to spontaneously assemble on smooth titanium oxide and titanium metal coated glass and silicon substrates, as well as on rough titanium metal implant surfaces. The surfaces were dipped in aqueous solutions of the corresponding ammonium salts for 48 h. The molecules are shown by X-ray photoelectron spectroscopy (XPS) to form densely packed, self-assembled monolayers (SAMs) on all surfaces investigated. The phosphate headgroups are believed to attach to the titanium (oxide) surface with the terminal end group (either methyl or hydroxy) pointing toward the ambient environment (air, vacuum, or water). Mixed SAMs are shown to be formed from mixed aqueous solutions of the two amphiphiles, with the hydroxy-terminated dodecyl phosphate adsorbing more favorably than the methyl-terminated molecule. The advancing water contact angles can be easily tailored via the composition of the self-assembly solution in the range of 110° (pure methyl) to 55° (pure hydroxy) on flat, smooth titanium surfaces. Surface roughness strongly modifies the wetting properties, with advancing contact angles in the range of 150−100° being observed, as well as the degree of hysteresis (difference between advancing and receding angles). Model calculations based on XPS intensities have been successfully used to quantify the adlayer composition and molecular surface densities across the whole range of mixed adlayer chemistry. The organophosphate monolayers on titanium are believed to have a significant potential for precise control of the surface chemistry and interfacial tension on both smooth and rough titanium surfaces in application areas such as medical implants and other devices where independent control of surface chemistry and topography is essential to performance.
Rotation Equivariant Vector Field Networks (2017)

In many computer vision tasks, we expect a particular behavior of the output with respect to rotations of the input image. If this relationship is explicitly encoded, instead of treated as any other variation, the complexity of the problem is decreased, leading to a reduction in the size of the required model. In this paper, we propose the Rotation Equivariant Vector Field Networks (RotEqNet), a Convolutional Neural Network (CNN) architecture encoding rotation equivariance, invariance and covariance. Each convolutional filter is applied at multiple orientations and returns a vector field representing magnitude and angle of the highest scoring orientation at every spatial location. We develop a modified convolution operator relying on this representation to obtain deep architectures. We test RotEqNet on several problems requiring different responses with respect to the inputs' rotation: image classification, biomedical image segmentation, orientation estimation and patch matching. In all cases, we show that RotEqNet offers extremely compact models in terms of number of parameters and provides results in line to those of networks orders of magnitude larger.