Miracle-dz/UniFAR-FTUs huggingface dataset:
Thrombin adhesive properties: induction by plasmin and heparan sulfate

We have previously demonstrated that chemically modified thrombin preparations induce endothelial cell (EC) adhesion, spreading and cytoskeletal reorganization via an Arg-Gly-Asp (RGD) sequence and the alpha v beta 3 integrin. Native thrombin, however, did not exhibit adhesive properties, consistent with crystal structure analysis, showing that Gly-Asp residues of the RGD epitope are buried within the molecule. We have now identified a possible physiological mean of converting thrombin to an adhesive protein. Plasmin, the major end product of the fibrinolytic system, converted thrombin to an adhesive protein for EC in a time and dose-dependent manner. EC adhesion and spreading was also induced by a low molecular weight (approximately 3,000 D) cleavage fragment generated upon incubation of thrombin with plasmin. Cell adhesion mediated by this fragment was completely inhibited by the synthetic peptide GRGDSP. Conversion of thrombin to an adhesive molecule was significantly enhanced in the presence of heparin or heparan sulfate, while other glycosaminoglycans (GAGs) (e.g., dermatan sulfate, keratan sulfate, chondroitin sulfate) had no effect. The role of cell surface heparan sulfate in thrombin conversion to EC adhesive protein was investigated using CHO cell mutants defective in various aspects of GAG synthesis. Incubation of both thrombin and a suboptimal amount of plasmin on the surface of formaldehyde fixed wild- type CHO-KI cells resulted in an efficient conversion of thrombin to an adhesive molecule, as indicated by subsequent induction of EC attachment. In contrast, there was no effect to incubation of thrombin and plasmin with fixed CHO mutant cells lacking both heparan sulfate and chondroitin sulfate, or with cells expressing no heparan sulfate and a three-fold increase in chondroitin sulfate. A similar gain of adhesive properties was obtained upon incubation of thrombin and plasmin in contact with native, but not heparinase-treated extracellular matrix (ECM) produced by cultured ECs. It appears that cell surface and ECM-associated heparan sulfate modulate thrombin adhesive properties through its heparin binding site in a manner that enables suboptimal amounts of plasmin to expose the RGD domain. Our results demonstrate, for the first time, a significant modulation of thrombin molecule by heparin, resulting in its conversion to a potent adhesive protein for ECs. This conversion is most effective in contact with cell surfaces, basement membranes and ECM.
The actin cytoskeleton in rapid steroid hormone actions

Early actin cytoskeleton reorganization is an important regulatory step of membrane‐initiated, non‐genomic steroid hormone actions. Specific intracellular signaling cascades control the rapid alterations of actin polymerization in a variety of cell models. Moreover, actin remodeling is a decisive component in the signaling of hormone‐induced early and late cellular responses. This article briefly summarizes the current knowledge on the steroid hormone‐induced early actin cytoskeleton rearrangements. It focuses on the current progress to characterize the glucocorticoid‐ and androgen‐initiated, tissue‐specific actin signaling pathways and discusses the plethora of cellular responses that are regulated by the early actin redistribution. It also provides insights into the potential clinical significance of actin dynamics and actin‐specific molecular signaling for nongenomic steroid hormone actions on tumor cells. © 2014 Wiley Periodicals, Inc.
PD-1/PD-L1 antibodies efficacy and safety versus docetaxel monotherapy in advanced NSCLC patients after first-line treatment option: systems assessment

Meta-analysis was conducted to systematically assess the effectiveness and safety of programmed cell death protein-1 or ligand-1 (PD-1 or PD-L1) antibodies versus docetaxel alone in advanced non small cell lung cancer (NSCLC). In addition, the prognostic significance of PD-L1 expression in advanced NSCLC was also investigated. 5 eligible studies including 3579 patients were identified through comprehensive search of multiple databases. The results showed that pooled hazard ratios (HR) for overall survival (OS) and progression free survival (PFS) were 0.69 (95% CI: 0.63-0.75; p < 0.001) and 0.87 (95% CI: 0.80-0.94; p < 0.001), between PD-1/PD-L1 antibodies and docetaxel treatment arms, respectively. The pooled relative risk (RR) value for objective response rate (ORR) was 1.53, (95% CI: 1.16-2.01, p = 0.003). Further, subgroup analysis based on PD-L1 expression indicated that pooled HR for OS was significant with 0.66(95% CI: 0.59-0.74, p < 0.001) for PD-L1≥1%. However, PD-L1 < 1% had HR value of 0.79 (95% CI: 0.67-0.93, p = 0.006). Our study concluded that advanced NSCLC patients benefited more with PD-1/PD-L1 antibodies than docetaxel in the second line treatment. PD-L1≥10% in tumor tissues is sufficient to show significant improvement in patient's outcome with PD-1/PD-L1 antibodies compared to docetaxel. Moreover, PD-1/PD-L1 antibodies treatment showed significant decrease in conventional chemotherapy adverse events, but increased immune-associated adverse effects.
Waste Nitrogen Excretion Via Amino Acid Acylation: Benzoate and Phenylacetate in Lysinuric Protein Intolerance

ABSTRACT: Benzoate and phenylacetate improve prognosis in inherited urea cycle enzyme deficiencies by increasing waste nitrogen excretion as amino acid acylation products. We studied metabolic changes caused by these substances and their pharmacokinetics in a biochemically different urea cycle disorder, lysinuric protein intolerance (LPI), under strictly standardized induction of hyperammonemia. Five patients with LPI received an intravenous infusion of 6.6 mmol/kg L-alanine alone and separately with 2.0 mmol/kg of benzoate or phenylacetate in 90 min. Blood for ammonia, serum urea and creatinine, plasma benzoate, hippurate, phenylacetate, phenylacetylglutamine, and amino acids was obtained at 0, 120, 180, and 270 min. Urine was collected in four consecutive 6-h periods. Alanine caused hyperammonemia: maximum increase 107, 28-411 µM (geometric mean, 95% confidence interval); ammonia increments were nearly identical after alanine + benzoate (60, 17-213 µM) and alanine + phenylacetate (79, 13-467 µM) (NS). Mean plasma benzoate was 6.0 mM when extrapolated to the end of alanine + benzoate infusions; phenylacetate was 4.9 mM at the end of alanine + phenylacetate. Transient toxicity (dizziness, nausea, vomiting) occurred in four patients at the end of combined infusions, and we suggest upper therapeutic plasma concentrations of 4.5 mM for benzoate and 3.5 mM for phenylacetate. Benzoate and phenylacetate then decreased following first-order kinetics with t1/2s of 273 and 254 min, respectively. Maximal plasma hippurate (0.24, 0.14-0.40 mM) was lower than maximal phenylacetylglutamine (0.48, 0.22-1.06 mM, p=0.008). Orotic acid excretion was 5.62, 1.84-17.14 µmol/kg per h after alanine, but only 1.07, 0.04-25.62 µmol/kg per h after alanine + benzoate (p<0.151) and 2.74,0.01-16.25 µmol/ kg per h after alanine + phenylacetate (p<0.016). Urea excretions were in the same range after all loads. Urinary hippurate nitrogen after alanine + benzoate and phenylacetylglutamine, nitrogen after alanine + phenylacetate accounted for an average of 12 and 22 of that in urea in the first 6 h. Of the benzoate and phenylacetate given, 65 and 51% were excreted in 24 h as hippurate and phenylacetyl-glutamine, respectively; less than 3.5% appeared unchanged in urine.
Who is where?: Matching People in Video to Wearable Acceleration During Crowded Mingling Events

We address the challenging problem of associating acceleration data from a wearable sensor with the corresponding spatio-temporal region of a person in video during crowded mingling scenarios. This is an important first step for multi-sensor behavior analysis using these two modalities. Clearly, as the numbers of people in a scene increases, there is also a need to robustly and automatically associate a region of the video with each person's device. We propose a hierarchical association approach which exploits the spatial context of the scene, outperforming the state-of-the-art approaches significantly. Moreover, we present experiments on matching from 3 to more than 130 acceleration and video streams which, to our knowledge, is significantly larger than prior works where only up to 5 device streams are associated.
A Wide Area Survey for High-Redshift Massive Galaxies. I. Number Counts and Clustering of BzKs and EROs

We present the results of a deep, wide area, optical and near-IR survey of massive high-redshift galaxies. The Suprime-Cam on the Subaru telescope was used to obtain BRIz′ imaging over 2 × 940 arcmin2 fields, while JKs imaging was provided by the SOFI camera at the New Technology Telescope (NTT) for a subset of the area, partly from the EIS. In this paper, we report on the properties of K-band-selected galaxies, identified from a total area of ~920 arcmin2 to KVega = 19, of which 320 arcmin2 are complete to KVega = 20. The BzK selection technique was used to assemble complete samples of about 500 candidate massive star-forming galaxies (sBzKs) and about 160 candidate massive passively evolving galaxies (pBzKs) at 1.4 ≲ z ≲ 2.5; and the (R - K)Vega > 5 color criterion was used to assemble a sample of about 850 extremely red objects (EROs). We accurately measure surface densities of 1.20 ± 0.05 and 0.38 ± 0.03 arcmin-2 for the sBzKs and the pBzKs, respectively. Both sBzKs and pBzKs are strongly clustered, at a level at least comparable to that of EROs, with pBzKs appearing more clustered than sBzKs. We estimate the reddening, star formation rates (SFRs), and stellar masses (M*) for the ensemble of sBzKs, confirming that to KVega ~ 20 typical (median) values are M* ~ 1011 M☉, SFR ~ 190 M☉ yr-1, and E(B - V) ~ 0.44. A correlation is detected such that the most massive galaxies at z ~ 2 are also the most actively star-forming, an effect that can be seen as a manifestation of downsizing at early epochs. The space density of massive pBzKs at z ~ 1.4-2 that we derive is 20% ± 7% that of similarly massive early-type galaxies at z ~ 0. Adding this space density to that of our massive star-forming class, sBzKs, in the same redshift range produces a closer comparison with the local early-type galaxy population, naturally implying that we are detecting star formation in a sizable fraction of massive galaxies at z > 1.4, which has been quenched by the present day. Follow-up optical and near-infrared spectroscopy is in progress at the ESO Very Large Telescope (VLT) and at the Subaru telescope in order to elucidate more thoroughly the formation and evolution of massive galaxies.
Anthropocene Crisis: Climate Change, Pollinators, and Food Security

In this paper, we propose a new approach—understood as a whole-of-community approach—to address a dualistic and dysfunctional human/nature relationship. Of particular concern is the decline in health and numbers of the insects that pollinate an estimated 90 percent of the Earth’s flora and an estimated 35 percent of global crop volume. Specifically, bees provide the majority of biotic pollination and play a critical role in food crop pollination. Multiple factors are contributing to this growing problem including a changing climate. In 2016, the International Commission on Stratigraphy agreed that the concept of the Anthropocene—the human epoch—is of sufficient scale to be considered part of the geological time scale. This indicates that these crises are not random or passive—they are largely the direct result of human activities. Despite decades of awareness of these socio-ecological issues, they continue to worsen. In addition, the growing awareness of the critical role of pollinators is creating a new understanding of our interconnectedness with the “natural” world. We introduce the Bee City movement as a way to operationalize a whole-of-community approach. Individual action is critical, but addressing pollinator health in these forums legitimizes and provides an institutional space for otherwise fringe, or even marginalized, activities and more coherent spaces for habitat creation.
Novel and Mechanical Stress–Responsive MicroRNAs in Populus trichocarpa That Are Absent from Arabidopsisw⃞

MicroRNAs (miRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes by targeting mRNAs for silencing. To test whether miRNAs play roles in the regulation of wood development in tree species, we isolated small RNAs from the developing xylem of Populus trichocarpa stems and cloned 22 miRNAs. They are the founding members of 21 miRNA gene families for 48 miRNA sequences, represented by 98 loci in the Populus genome. A majority of these miRNAs were predicted to target developmental- and stress/defense-related genes and possible functions associated with the biosynthesis of cell wall metabolites. Of the 21 P. trichocarpa miRNA families, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental expression patterns, suggesting that even conserved miRNAs may have different regulatory roles in different species. Most unexpectedly, the remaining 10 miRNAs, for which 17 predicted targets were experimentally validated in vivo, are absent from the Arabidopsis genome, suggesting possible roles in tree-specific processes. In fact, the expression of a majority of the cloned miRNAs was upregulated or downregulated in woody stems in a manner consistent with tree-specific corrective growth against tension and compression stresses, two constant mechanical loads in trees. Our results show that plant miRNAs can be induced by mechanical stress and may function in one of the most critical defense systems for structural and mechanical fitness.
Geriatric falls in the context of a hospital fall prevention program: delirium, low body mass index, and other risk factors

Background Inpatient geriatric falls are a frequent complication of hospital care that results in significant morbidity and mortality. Objective Evaluate factors associated with falls in geriatric inpatients after implementation of the fall prevention program. Methods Prospective observational study comprised of 788 consecutive patients aged 79.5±7.6 years ( χ¯ ± standard deviation) (66% women and 34% men) admitted to the subacute geriatric ward. Comprehensive geriatric assessment (including Mini-Mental State Examination, Barthel Index of Activities of Daily Living, and modified Get-up and Go Test) was performed. Confusion Assessment Method was used for diagnosis of delirium. Patients were categorized into low, moderate, or high fall risk groups after clinical and functional assessment. Results About 15.9%, 21.1%, and 63.1% of participants were classified into low, moderate, and high fall risk groups, respectively. Twenty-seven falls were recorded in 26 patients. Increased fall probability was associated with age ≥76 years (P<0.001), body mass index (BMI) <23.5 (P=0.007), Mini-Mental State Examination <20 (P=0.004), Barthel Index <65 (P=0.002), hemoglobin <7.69 mmol/L (P=0.017), serum protein <70 g/L (P=0.008), albumin <32 g/L (P=0.001), and calcium level <2.27 mmol/L. Four independent factors associated with fall risk were included in the multivariate logistic regression model: delirium (odds ratio [OR] =7.33; 95% confidence interval [95% CI] =2.76–19.49; P<0.001), history of falls (OR =2.55; 95% CI =1.05–6.19; P=0.039), age (OR =1.14; 95% CI =1.05–1.23; P=0.001), and BMI (OR =0.91; 95% CI =0.83–0.99; P=0.034). Conclusion Delirium, history of falls, and advanced age seem to be the primary risk factors for geriatric falls in the context of a hospital fall prevention program. Higher BMI appears to be associated with protection against inpatient geriatric falls.
CA19-9 elevation in ovarian mature cystic teratoma: Discrimination from ovarian cancer – CA19-9 level in teratoma

Background We aimed to identify clinical characteristics of ovarian mature cystic teratoma (MCT) in association with CA19-9 elevation, and to determine if CA19-9 is a useful marker in discrimination of MCT from ovarian cancer (OC). Material/Methods Medical records of 322 women with pathologically-confirmed MCT or OC (stage 1 or 2) were reviewed retrospectively. The relationships between the characteristics of MCT (mean diameter, bilaterality, and pathologic components) and elevated CA19-9 were evaluated. Tumor markers in MCT were compared to those in OC. Results MCTs with CA19-9 elevation were correlated with a larger diameter (8.53±3.84 cm vs. 6.95±3.97 cm, p=0.002) and presence of fat component (67.1% vs. 32.9%, p<0.001), compared to those with normal CA 19-9. Although the incidence of CA19-9 elevation was not different between patients with MCT and OC (p=0.700), the mean value of CA19-9 was higher in those with OC (114.66±20.66 U/mL vs. 508.58±261.63 U/mL, p=0.013). In addition, simultaneous elevation of CA125 and CA19-9 was associated with a higher probability of malignant neoplasm (p<0.001; odds ratio: 23.7; 95% confidence interval: 8.863–63.576) than single elevation of CA 19-9. Conclusions CA19-9 could be an important tool in the diagnosis of ovarian mature cystic teratoma. CA19-9, in combination with CA125, might be a useful marker in discrimination of MCT from cancer.
Selection: Salience, Relevance and the Coupling between Domain-Level Tasks and Text Planning

In this paper we examine some issues pertaining to the task of selection in text planning. We attempt to distinguish salience and relevance, and characterize their role as important fundamental notions governing selection. We also formulate the problem of selection of text content in terms of the coupling between domain-level tasks and text planning tasks. We describe our research on generating bus route descriptions.
The Relationship between Project-Based Learning and Rigor in STEM-Focused High Schools.

Project-based learning (PjBL) is an approach often favored in STEM classrooms, yet some studies have shown that teachers struggle to implement it with academic rigor. This paper explores the relationship between PjBL and rigor in the classrooms of ten STEM-oriented high schools. Utilizing three different data sources reflecting three different perceptions—student surveys, teacher logs, and classroom observations—the study examines the extent to which PjBL and rigor co-occur. Across all three measures, the results show that use of PjBL is associated with higher levels of rigor. However, the study also shows that academic rigor can be present in the absence of PjBL, and that PjBL can be implemented with low levels of rigor. The paper concludes with implications for practice.
Accumulation of Viral Transcripts and DNA during Establishment of Latency by Herpes Simplex Virus

ABSTRACT Latent infection of mice with wild-type herpes simplex virus is established during an acute phase of ganglionic infection in which there is abundant viral replication and productive-cycle gene expression. Thymidine kinase-negative mutants establish latent infections but are severely impaired for acute ganglionic replication and productive-cycle gene expression. Indeed, by in situ hybridization assays, acute infection by these mutants resembles latency. To assess events during establishment of latency by wild-type and thymidine kinase-negative viruses, we quantified specific viral nucleic acid sequences in mouse trigeminal ganglia during acute ganglionic infection by using sensitive PCR-based assays. Through 32 h postinfection, viral DNA and transcripts representative of the three kinetic classes of productive-cycle genes accumulated to comparable levels in wild-type- and mutant-infected ganglia. At 48 and 72 h, although latency-associated transcripts accumulated to comparable levels in ganglia infected with wild-type or mutant virus, levels of DNA accumulating in wild-type-infected ganglia exceeded those in mutant-infected ganglia by 2 to 3 orders of magnitude. Coincident with this increase in DNA, wild-type-infected ganglia exhibited abundant expression of productive-cycle genes and high titers of infectious progeny. Nevertheless, the levels of productive-cycle RNAs expressed by mutant virus during acute infection greatly exceeded those expressed by wild-type virus during latency. The results thus distinguish acute infection of ganglia by a replication-compromised mutant from latent infection and may have implications for mechanisms of latency.
Characterization and application of single fluorescent nanodiamonds as cellular biomarkers

Type Ib diamonds emit bright fluorescence at 550–800 nm from nitrogen-vacancy point defects, (N-V)0 and (N-V)−, produced by high-energy ion beam irradiation and subsequent thermal annealing. The emission, together with noncytotoxicity and easiness of surface functionalization, makes nano-sized diamonds a promising fluorescent probe for single-particle tracking in heterogeneous environments. We present the result of our characterization and application of single fluorescent nanodiamonds as cellular biomarkers. We found that, under the same excitation conditions, the fluorescence of a single 35-nm diamond is significantly brighter than that of a single dye molecule such as Alexa Fluor 546. The latter photobleached in the range of 10 s at a laser power density of 104 W/cm2, whereas the nanodiamond particle showed no sign of photobleaching even after 5 min of continuous excitation. Furthermore, no fluorescence blinking was detected within a time resolution of 1 ms. The photophysical properties of the particles do not deteriorate even after surface functionalization with carboxyl groups, which form covalent bonding with polyl-lysines that interact with DNA molecules through electrostatic forces. The feasibility of using surface-functionalized fluorescent nanodiamonds as single-particle biomarkers is demonstrated with both fixed and live HeLa cells.
Finite-difference time-domain simulation of the Maxwell-Schrödinger system

A thorough study on the finite-difference time-domain (FDTD) simulation of the Maxwell-Schrödinger system in the semi-classical regime is given. For the Maxwell part which is treated classically, an alternative approach directly using the vector and scalar potentials (A and Φ) is taken. This approach is stable in the long wavelength regime and removes the need to extract the potentials at every time step. Perfectly matched layer (PML) is developed for this system. For the Schrödinger and quantum mechanical part, minimal coupling is applied to couple the charges to the electromagnetic potentials. Simulation results agree with the theory of quantum coherent states.
The Clarification of Depression and Social Support’s Contribution to the Prediction of Antiretroviral Medication Adherence and the Rate of CD4 in People with HIV

With the development of the antiretroviral therapy, the number of the people with HIV is increasing; therefore, identifying the factors affecting HIV is of great importance. This study aimed to investigate the relationship between the antiretroviral medication adherence and the rate of CD4 with depression and social support in the people with HIV. The research method was a descriptive study kind of correlation. The statistical population included all patients with HIV in Shiraz, of whom, 220 people who had referred to the Behavioral Diseases Consultation Center were selected using the available sampling method. Philips et al.’s Social Support Questionnaire, Beck’s Depression Questionnaire II, and ACTG Medication Adherence Questionnaire were used as the research tools. Results were analyzed using the stepwise regression and stepwise hierarchical multiple regression. Regression analysis showed that social support and depression variables could predict totally 47% (P<0.001) of changes of medication adherence variable, and depression could predict only 2% (P<0.01) of rate variance of CD4.