Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a Minimum Enhancer Sequence for the Type II Collagen Gene Reveals Several Core Sequence Motifs in Common with the Link Protein Gene (*)

The type II collagen gene (Col2a1) is expressed primarily in chondrocytes. Transcription of Col2a1 is mediated by cell-specific regulatory elements located within the promoter and first intron. Here, we map a minimal enhancer and identify elements that determine cartilage-specific Col2a1 expression by analyzing the activity of a series of chimeric genes consisting of rat Col2a1 first intron deletion mutants ligated to the chloramphenicol acetyltransferase reporter gene. We show that a 100-base pair (bp) segment within the first intron is the minimum size necessary for high level, cell type-specific expression of Col2a1. Sequence analysis of this 100-bp Col2a1 enhancer revealed several sequence motifs similar to motifs present within the regulatory region of the link protein gene, another cartilage gene. These motifs include an AT-rich element, a C1 motif and a C3 motif. Deletion of any of these elements reduced Col2a1 enhancer activity in chick embryo chondrocytes. We also tested enhancer-mediated activity in CFK2 cells which differentiate to a chondrogenic phenotype and begin to express type II collagen mRNA after extended culture. In stably transfected CFK2 cells, constructs containing the 100-bp enhancer were activated during the transition from prechondrogenic to chondrogenic cell populations and deletions within the enhancer strongly down-regulated activity. Chondrocyte-specific DNA-protein complexes were identified using nuclear extracts prepared from chick embryo chondrocytes and P-labeled oligonucleotides from these regions of the first intron. These results suggest that interaction of chondrocyte specific nuclear factors with multiple core elements from a small region within the first intron are important for cell-type specific Col2a1 enhancer activity.
Development of 3–5 THz harmonic mixer

There is a high need for >2 THz room temperature direct-detectors/harmonic-mixers to characterize THz optical sources, phase lock THz-QCLs as LO sources for multi-pixel receivers, and realize absolute frequency calibration sources for applications in astrophysics, earth science, and remote sensing. Thus, we have developed a WM-52 (WR-0.22) harmonic mixer for the 3–5 THz operation. The design, fabrication and assembly of the THz mixer are discussed.
Fluorescence activated cell sorting.

An instrument has been developed for sorting biological cells. The cells are rendered differentially fluorescent and incorporated into a small liquid stream illuminated by a laser beam. The cells pass sequentially through the beam, and fluorescent light from the cells gives rise to electrical signals. The stream is broken into a series of uniform size drops downstream of the laser. The cell signals are used to give appropriate electrostatic charges to drops containing the cells. The drops then pass between two charged plates and are deflected to appropriate containers. The system has proved capable of providing fractions containing large numbers of viable cells highly enriched in a particular functional type.
Polyamines and Ca2+ Mediate Hyperosmolal Opening of the Blood‐Brain Barrier: In Vitro Studies in Isolated Rat Cerebral Capillaries

Abstract We recently presented evidence that the reversible opening of the blood‐brain barrier (BBB) by the infusion of 1.6 M mannitol into the rat internal carotid artery is mediated by a rapid stimulation of ornithine decarboxylase (ODC) activity and putrescine synthesis in cerebral capillaries. We have now investigated this hypothesis further, using isolated rat cerebral capillaries as an in vitro model of the BBB. The ODC activity of cerebral capillary preparations was enriched up to 15‐fold over that of the cerebral homogenate. Hyperosmolal mannitol in physiological buffer evoked a rapid (<15 s), concentration‐ and time‐dependent increase in capillary ODC activity and an accumulation of putrescine and spermidine which was blocked by the specific ODC inhibitor, α‐ difluoromethylornithine (DFMO, 10 m M). Mannitol (1 M), as well as 2 M urea, evoked a two‐ to fivefold increase in the temperature‐sensitive influx of 45Ca2+ and uptake of horseradish peroxidase (HRP) and 2‐deoxy‐D‐[1‐3H]glucose (DG), but not α‐[1‐14C]aminoisobutyrate, during a 2‐min incubation. DFMO (10 mM) abolished 1 M mannitol‐mediated stimulation of 45Ca2+ influx and uptake of HRP and DG, whereas 1 mM putrescine replenished capillary polyamines and reversed the DFMO effects. Mannitol (1 M)‐induced stimulation of ODC activity and membrane transport processes was Ca2+‐dependent and verapamil‐ and nisoldipine‐sensitive. Phorbol myristate acetate (PMA, 10 nM), a protein kinase C activator, also evoked a two‐ to threefold stimulation of 45Ca2+ transport and HRP and DG uptake. This PMA effect was abolished by DFMO, suggesting involvement of rapid, ODC‐controlled polyamine synthesis. The effects of 10 nM PMA and 1 M mannitol were additive, suggesting that hyperosmolal stimulation of ODC‐activated polyamine synthesis does not involve protein kinase C. These data support the hypothesis that ODC‐activated polyamine synthesis and Ca2+ influx (via Ca2+ channels) play a key role in mediating the effects of hyperosmolality on BBB permeability.
Image Captioning using Visual Attention

This aim of this project is to generate descriptive captions for images using neural language models. Deep learning has been used via a Convolutional Neural Network coupled with an LSTM based architecture. An image is passed on as an input to the CNN, which yields certain annotation vectors. Based on a human vision inspired notion of attention, a context vector is obtained as a function of these annotation vectors, which is then passed as an input to the LSTM. The LSTM network training is separately performed with randomly initialised word and phrase embeddings respectively. The output, thereby, obtained is passed to a softmax layer to generate captions. Our results have been evaluated using a metric named Meteor, and word embedding based implementation turns out to be better than its phrase embedding based counterpart.
A Flexible Model for Locating Services on the Web

The new SOA paradigm will increase the number of available services, possibly creating a location and use bottleneck. A model for the effective location of services is proposed. Its prototype implementation has features applicable to heterogeneous usage scenarios: (1) flexible descriptions of services and goals, (2) assistance to consumers and providers in describing services sought and offered, and (3) trade-offs between accuracy of results and efficiency of the location process based on the application of different filters.
Influence of a substance-abuse-prevention curriculum on violence-related behavior.

OBJECTIVE To test the impact of a school-based substance-abuse-prevention program, Project Towards No Drug Abuse (TND), on risk for violence. METHODS Logistic regression analyses tested whether victimization, perpetration, or weapon carrying differed for intervention students relative to control students within a sample of 850 continuation high school students followed over 12 months. RESULTS We observed a higher risk for victimization (OR=1.57) among male control students. No intervention effect was observed for female students or for perpetration among males. CONCLUSION The findings provide limited support for a generalization of TND's preventive effect.
Characterization of a human Kaposi's sarcoma cell line that induces angiogenic tumors in animals

ObjectiveTo characterize a Kaposi's sarcoma (KS) cell line established from a tumor biopsy from the oral mucosa of an iatrogenically immunosuppressed HIV-negative man. MethodsCells were placed in culture and evaluated by a variety of biologic, serologic, karyotypic, and immunologic procedures. Electron microscopic examination was performed. The ability to produce tumors in nude mice was evaluated, and the nature of the cells within the tumor determined. Assays for urokinase plasminogen activator type (uPA), plasminogen activator inhibitor-1 (PAI-1) and the urokinase receptor (uPAR) were conducted. ResultsThe SLK cell line has an endothelial cell morphology with very little anaplasia. The karyotype indicates diploid phenotype of human origin. Immunohistochemical and electron microscopic examinations confirmed the endothelial nature of this cell line. No viruses were detected. The tumors induced in nude mice showed hypervascularization, with characteristics of KS. The cell line produces uPA and PAI-1, and also expresses uPAR. ConclusionsThe SLK cell line is of endothelial cell origin and the first human cell line to induce KS-like tumors in recipient animals. The expression of urokinase and its receptor suggests a paracrine and autocrine interaction that may be important for the growth of the tumor. The SLK line should be valuable for studies of KS pathogenesis and therapeutic approaches to this malignancy.
Na/K-ATPase β1 Subunit Expression Is Required for Blastocyst Formation and Normal Assembly of Trophectoderm Tight Junction-associated Proteins*

Na/K-ATPase plays an important role in mediating blastocyst formation. Despite the expression of multiple Na/K-ATPase α and β isoforms during mouse preimplantation development, only the α1 and β1 isoforms have been localized to the basolateral membrane regions of the trophectoderm. The aim of the present study was to selectively down-regulate the Na/K-ATPase β1 subunit employing microinjection of mouse 1 cell zygotes with small interfering RNA (siRNA) oligos. Experiments comprised of non-injected controls and two groups microinjected with either Stealth™ Na/K-ATPase β1 subunit oligos or nonspecific Stealth™ siRNA as control. Development to the 2-, 4-, 8-, and 16-cell and morula stages did not vary between the three groups. However, only 2.3% of the embryos microinjected with Na/K-ATPase β1 subunit siRNA oligos developed to the blastocyst stage as compared with 73% for control-injected and 91% for non-injected controls. Na/K-ATPase β1 subunit down-regulation was validated by employing reverse transcription-PCR and whole-mount immunofluorescence methods to demonstrate that Na/K-ATPase β1 subunit mRNAs and protein were not detectable in β1 subunit siRNA-microinjected embryos. Aggregation chimera experiments between β1 subunit siRNA-microinjected embryos and controls demonstrated that blockade of blastocyst formation was reversible. The distribution of Na/K-ATPase α1 and tight junction-associated proteins occludin and ZO-1 were compared among the three treatment groups. No differences in protein distribution were observed between control groups; however, all three polypeptides displayed an aberrant distribution in Na/K-ATPase β1 subunit siRNA-microinjected embryos. Our results demonstrate that the β1 subunit of the Na/K-ATPase is required for blastocyst formation and that this subunit is also required to maintain a normal Na/K-ATPase distribution and localization of tight junction-associated polypeptides during preimplantation development.
Oxidative stress in asphyxiated term infants resuscitated with 100% oxygen.

OBJECTIVE To test the hypothesis that resuscitation of asphyxiated infants with pure oxygen causes hyperoxemia and oxidative stress.Study design Asphyxiated term newborn infants (n = 106) were randomly resuscitated with room air (RAR = 51) or 100% oxygen (OxR = 55). The Apgar score, time of the first cry, and establishment of a sustained pattern of respiration were recorded. Assays performed included: blood gases; reduced glutathione (GSH) and oxidized glutathione (GSSG) in whole blood; glutathione-related enzyme activities; and superoxide dismutase activity (SOD) in erythrocytes. RESULTS The RAR group needed less time of ventilation for resuscitation (5.3 +/- 1.5 vs 6.8 +/- 1.2 min; P <.05). Pure oxygen caused hyperoxemia (PO(2), 126.3 +/- 21.8 mm Hg) that did not occur with the use of room air (PO(2), 72.2 +/- 6.8 mm Hg). GSH was decreased and GSSG, the glutathione cycle enzymes, and SOD activities were increased in both asphyxiated groups. However, the 100% oxygen-resuscitated group showed significantly greater alterations that correlated positively with hyperoxemia. CONCLUSIONS Asphyxia causes oxidative stress in the perinatal period, and resuscitation with 100% oxygen causes hyperoxemia and increased oxidative stress. Because there are no advantages to resuscitation with 100% oxygen, room air may be preferred under certain circumstances for the resuscitation of asphyxiated neonates.
Description of Bullera kunmingensis sp. nov., and clarification of the taxonomic status of Bullera sinensis and its synonyms based on molecular phylogenetic analysis.

A ballistoconidium-forming yeast strain, CH 2.506, isolated from a semi-dried leaf of Parthenocissus sp. collected near Kunming City in Yunnan, China, was shown to be closely related to the non-ballistoconidium-forming species Cryptococcus luteolus (Saito) C.E. Skinner and the ballistoconidium-forming species Bullera sinensis Li by molecular phylogenetic analysis based on 18S rDNA sequencing. This strain was demonstrated to represent a distinct undescribed yeast species by internal transcribed spacer (ITS) region sequence and G+C content comparison and DNA-DNA relatedness, for which the name Bullera kunmingensis sp. nov. is proposed. Meanwhile, the taxonomic relationships among Bullera sinensis and its synonyms B. derxii Nakase & Suzuki and B. alba (Hanna) Derx var. lactis Li, were clarified on the basis of molecular phylogenetic analysis and DNA-DNA reassociation. B. derxii was confirmed to be conspecific with B. sinensis, while B. alba var. lactis was shown to represent a variety of B. sinensis. A new combination, Bullera sinensis Li var. lactis (Li) Bai, Takashima et Nakase, is therefore proposed. Comparative analysis of different types of molecular criteria employed in the present study suggested that when inferring phylogenetic relationships among sibling taxa, sequence data from ITS regions should be interpreted with caution.
Arterial Wall Changes in Type 2 Diabetic Subjects

Arterial ultrasonic appearances using high resolution ultrasound were studied in 97 subjects with Type 2 diabetes and age‐ and sex‐matched controls. The intima‐media thickness of both common carotid arteries was measured 2 cm proximal to the bifurcation and the presence or absence of plaque on both common and femoral bifurcations was recorded. The mean intima‐media thickness in subjects with diabetes was 0.82 ± 0.22 mm while in the controls 0.66 ± 0.13 mm (p < 0.001). Multiple regression in diabetic subjects only showed no correlation between age, sex, body mass index, smoking, duration of diabetes, systolic or diastolic blood pressure, cholesterol, HDL, LDL, triglycerides, HbA, and the common carotid artery intima‐media thickness. Type 2 diabetes is associated with increased intima‐media thickness which has been found to be a marker of cardiovascular events in the general population.
Coherent quantum oscillations and echo measurements of a Si charge qubit

Fast quantum oscillations of a charge qubit in a double quantum dot fabricated in a Si/SiGe heterostructure are demonstrated and characterized experimentally. The measured inhomogeneous dephasing time T2* ranges from 127 ps to 2.1 ns; it depends substantially on how the energy difference of the two qubit states varies with external voltages, consistent with a decoherence process that is dominated by detuning noise (charge noise that changes the asymmetry of the qubit's double-well potential). In the regime with the shortest T2*, applying a charge-echo pulse sequence increases the measured inhomogeneous decoherence time from 127 to 760 ps, demonstrating that low-frequency noise processes are an important dephasing mechanism.
Kinectin-Kinesin Binding Domains and Their Effects on Organelle Motility*

Intracellular organelle motility involves motor proteins that move along microtubules or actin filaments. One of these motor proteins, kinesin, was proposed to bind to kinectin on membrane organelles during movement. Whether kinectin is the kinesin receptor on organelles with a role in organelle motility has been controversial. We have characterized the sites of interaction between human kinectin and conventional kinesin using in vivo and in vitro assays. The kinectin-binding domain on the kinesin tail partially overlaps its head-binding domain and the myosin-Va binding domain. The kinesin-binding domain on kinectin resides near the COOH terminus and enhances the microtubule-stimulated kinesin-ATPase activity, and the overexpression of the kinectin-kinesin binding domains inhibited kinesin-dependent organelle motility in vivo. These data, when combined with other studies, suggest a role for kinectin in organelle motility.
Mathematical modelling of avascular-tumour growth. II: Modelling growth saturation.

We build on our earlier mathematical model (Ward & King, 1997, IMA J. Appl. Math Appl. Med. Biol., 14, 39-69) by incorporating two necrotic depletion mechanisms, which results in a model that can predict all the main phases of avascular-tumour growth and heterogeneity. The model assumes a continuum of live cells which, depending on the concentration of a generic nutrient, may reproduce or die, generating local volume changes and thus producing movement described by a velocity field. The necrotic material is viewed as basic cellular material (i.e. as a generic mix of proteins, DNA, etc.) which is able to diffuse and is utilized by living cells as raw material to construct new cells during mitosis. Numerical solution of the resulting system of partial differential equations shows that growth ultimately tends either to a steady-state (growth saturation) or becomes linear. Both the travelling-wave and steady-state limits of the model are therefore derived and studied. The analysis demonstrates that, except in a very special case, passage of cellular material across the tumour surface is necessary for growth saturation to occur. Using numerical techniques, the domains of existence of the large-time solutions are explored in parameter space. For a particular limit, asymptotic analysis makes explicit the main phases of growth and gives the location of the bifurcation between the long-time outcomes.
An assessment of E-Learning readiness using multi-dimensional model

E-Learning readiness in a university need to be measured in order to obtain description on how well the preparation of the university in implementing e-learning. This study presents a methodology in measuring e-learning readiness using multi-dimensional model. Assessment was conducted through questionnaires and data analysis. The instrument contains a set of e-learning readiness indicators that cover five domains and thirteen factors. The assessment result can provide a comprehensive representation for institution regarding its current condition and a reference for future improvement. It also can provide a description about which factors that are needed to be prioritized. E-learning implementation in Telkom University was selected as case studies to be assessed. The assessment result was acquire Priority Index and Readiness Index, which describes the level of readiness in Telkom University. The result highlights four priority factors, namely hardware, learning methods and learning content. Meanwhile, Telkom University has some factors to be improved regarding e-learning implementation. According to the respondents, respondents considered that learning content, administration and business are factors that not yet ready.
An Overview of Prosodic Modelling for Croatian Speech Synthesis

In order to include prosody into the text to speech (TTS)systems prosody knowledge needs to be acquired, represented and incorporated. Two main features of prosody important for modelling prosody for TTS systems are duration and F0 contour. There are various approaches to modelling those features and they can be categorized into three main groups: rule based, statistical and minimalistic. Some of the best known approaches to duration acquiring are Klatt’ s model, classification and regression trees (CARTS) and neural networks and to F0 modelling TOBI, Fujisaki and Tilt. A procedure for automatic intonation event detection on Croatian texts based on the Tilt model was evaluated in terms of Root Mean Square Error values for generated F0 contours.
Computational performance improvements of multiple hypothesis tracking algorithm

Multiple hypothesis tracking (MHT) is considered to be the preferred solution for track formation and target tracking in complex environment. Main difficulty with MHT is it's high computing power requirements. This paper deals with several aspects of computational performance of this algorithm. Improvements like space division, multithread processing and fast hypotheses generation techniques are considered.
Molecular and Functional Evidence for Multiple Ca2+-binding Domains in the Type 1 Inositol 1,4,5-Trisphosphate Receptor*

Structural and functional analyses were used to investigate the regulation of the inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R) by Ca2+. To define the structural determinants for Ca2+ binding, cDNAs encoding GST fusion proteins that covered the complete linear cytosolic sequence of the InsP3R-1 were expressed in bacteria. The fusion proteins were screened for Ca2+ and ruthenium red binding through the use of 45Ca2+ and ruthenium red overlay procedures. Six new cytosolic Ca2+-binding regions were detected on the InsP3R in addition to the one described earlier (Sienaert, I., De Smedt, H., Parys, J. B., Missiaen, L., Vanlingen, S., Sipma, H., and Casteels, R. (1996)J. Biol. Chem. 271, 27005–27012). Strong45Ca2+ and ruthenium red binding domains were localized in the N-terminal region of the InsP3R as follows: two Ca2+-binding domains were located within the InsP3-binding domain, and three Ca2+ binding stretches were localized in a 500-amino acid region just downstream of the InsP3-binding domain. A sixth Ca2+-binding stretch was detected in the proximity of the calmodulin-binding domain. Evidence for the involvement of multiple Ca2+-binding sites in the regulation of the InsP3R was obtained from functional studies on permeabilized A7r5 cells, in which we characterized the effects of Ca2+ and Sr2+ on the EC50 and cooperativity of the InsP3-induced Ca2+ release. The activation by cytosolic Ca2+was due to a shift in EC50 toward lower InsP3concentrations, and this effect was mimicked by Sr2+. The inhibition by cytosolic Ca2+ was caused by a decrease in cooperativity and by a shift in EC50 toward higher InsP3 concentrations. The effect on the cooperativity occurred at lower Ca2+ concentrations than the inhibitory effect on the EC50. In addition, Sr2+ mimicked the effect of Ca2+ on the cooperativity but not the inhibitory effect on the EC50. The different [Ca2+] and [Sr2+] dependencies suggest that three different cytosolic interaction sites were involved. Luminal Ca2+ stimulated the release without affecting the Hill coefficient or the EC50, excluding the involvement of one of the cytosolic Ca2+-binding sites. We conclude that multiple Ca2+-binding sites are localized on the InsP3R-1 and that at least four different Ca2+-interaction sites may be involved in the complex feedback regulation of the release by Ca2+.