Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of E-cadherin Expression on Hormone Production in Rat Anterior Pituitary Lactotrophs In Vitro

Cadherins are a family of transmembrane glycoproteins that mediate cell-to-cell adhesion. A change in cadherin type in cells, i.e., cadherin switching, induces changes in the character of the cell. Recent studies of the developing rat adenohypophysis found that primordial cells co-expressed E- and N-cadherins, but that hormone-producing cells lost E-cadherin and ultimately possessed only N-cadherin. In the present study, we examined the roles of cadherin switching in cytogenesis of anterior pituitary cells by observing prolactin mRNA and protein expression in lactotrophs that were transformed with an E-cadherin expression vector. In hormone-producing cells that were transfected with a pIRES2-ZsGreen1 plasmid with a full-length E-cadherin cDNA (rE-cad-IZ) insert in primary culture, we detected E- and N-cadherins on plasma membrane and E-cadherin in cytoplasm. In these rE-cad-IZ-transfected cells, in situ hybridization revealed prolactin mRNA signals that were at a level identical to that in control cells, while prolactin protein was barely detectable using immunocytochemistry. The mean signal intensity of prolactin protein in rE-cad-IZ-transfected cells was approximately one fourth that in intact cells and in null-IZ-transfected cells (P<0.01). These results suggest that the expression of E-cadherin does not affect prolactin mRNA transcription; rather, it reduces prolactin protein content, presumably by affecting trafficking of secretory granules.
Comparison of risk indicators of dental caries in children with and without cleft lip and palate deformities

Objective: To test the hypothesis that there are no differences in various risk factors of dental caries among children with cleft lip and palate when compared to non-cleft high caries risk and non-cleft caries free children. Design: Seventy-three children in the age range of 4-9 years comprised three groups; Group-I (n = 23, children with cleft lip and palate), Group-II (n = 25, non-cleft high caries risk children) and Group-III (n = 25, non-cleft caries free children). Various risk factors for dental caries like type of oral hygiene practice, sugar exposures/day, developmental defects of enamel, caries activity, salivary streptococci mutans levels and lactobacilli levels were evaluated and compared among the three groups of children. Results: The mean deft score among Group-II children was significantly more (P < 0.01) as compared to the Group-I children. The mean deft + DMFT score among Group-I and Group-II children was comparable (P = 0.149). Developmental enamel defects were more among Group-I children as compared to Group-II and Group-III children (P < 0.01). Hypoplasia of the maxillary anterior teeth was more common among Group-I children as compared to Group-II (P < 0.05) and Group-III children (P < 0.001). The association between hypoplastic teeth and dental caries was significant (P < 0.05). The salivary acidogenic potential as evaluated by Snyder test was comparable among Group-I and Group-II children. The salivary streptococcus mutans levels in Group-I and Group-II children were higher when compared to lactobacillus counts. Conclusion: The risk factors of dental caries among children with cleft lip and palate were more as compared to non-cleft high caries risk and non-cleft caries free children.
Towards the Extraction of Domain Concepts from the Identifiers

Program identifiers represent an invaluable source of information for developers who are not familiar with the code to be evolved. Domain concepts and inter-concept relationships can be automatically extracted by means of natural language processing techniques applied to the program identifiers. However, the ontology produced by this approach tends to be very large and to include implementation details that reduce its usefulness for domain concept understanding. In this paper, we analyze the effectiveness of information retrieval based techniques used to filter domain concepts and relations from the implementation details, so as to obtain a smaller, more informative domain ontology. In particular, we show that fully automated techniques based on keywords or topics have quite poor performance, while a semi-automated approach, requiring limited user involvement, can highly improve the filtering of domain concepts.
Real-time bioacoustics monitoring and automated species identification

Traditionally, animal species diversity and abundance is assessed using a variety of methods that are generally costly, limited in space and time, and most importantly, they rarely include a permanent record. Given the urgency of climate change and the loss of habitat, it is vital that we use new technologies to improve and expand global biodiversity monitoring to thousands of sites around the world. In this article, we describe the acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON), a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings. The major components of the cyberinfrastructure include: a solar powered remote monitoring station that sends 1-min recordings every 10 min to a base station, which relays the recordings in real-time to the project server, where the recordings are processed and uploaded to the project website (arbimon.net). Along with a module for viewing, listening, and annotating recordings, the website includes a species identification interface to help users create machine learning algorithms to automate species identification. To demonstrate the system we present data on the vocal activity patterns of birds, frogs, insects, and mammals from Puerto Rico and Costa Rica.
Impaired Visuospatial Short-Term Memory in Children with ADHD

ABSTRACT Previous studies provide clear evidence that visuospatial memory performance in children with attention-deficit/hyperactivity disorder (ADHD) is significantly lower than in typically developing children. In the present study, we investigated a major cause of their low performance using a spatial span test. Possibly, inattention resulting from lack of motivation or interest causes their low performance so that they do not correctly encode targets to be remembered. On the other hand, a deficit in temporary maintenance per se may cause their low performance; that is, their inefficient use of rehearsal during a retention interval may lead to memory traces’ fast decay. Results in this study indicated that children with ADHD could sustain attention during the encoding phase. Furthermore, their performance at delayed recall was significantly lower than immediate recall, but delayed recall did not affect typically developing children's performance. These results provide evidence for the likelihood that a factor causing children with ADHD difficulty in temporarily maintaining visuospatial information is fast decay of memory traces as a result of inefficient use of rehearsal, not inattention in the encoding phase.
Pajek - Program for Large Network Analysis

Large networks, having thousands of vertices and lines, can be found in many different areas, e. g: genealogies, flo w graphs of programs, molecule, computer networks, transportation networks, social networks, intra/inter organisational networks . Many standard network algorithms are very time and space consuming and therefore unsuitable for analysis of such networks. In the article we present some approaches to analysis and visualisation of large networks implemented in programPajek. Some typical examples are also given.
Adeno-associated virus 2-mediated high efficiency gene transfer into immature and mature subsets of hematopoietic progenitor cells in human umbilical cord blood

Recombinant adeno-associated virus 2 (AAV) virions were constructed containing a gene for resistance to neomycin (neoR), under the control of either the herpesvirus thymidine kinase (TK) gene promoter (vTK- Neo), or the human parvovirus B19 p6 promoter (vB19-Neo), as well as those containing an upstream erythroid cell-specific enhancer (HS-2) from the locus control region of the human beta-globin gene cluster (vHS2-TK-Neo; vHS2-B19-Neo). These recombinant virions were used to infect either low density or highly enriched populations of CD34+ cells isolated from human umbilical cord blood. In clonogenic assays initiated with cells infected with the different recombinant AAV-Neo virions, equivalent high frequency transduction of the neoR gene into slow-cycling multipotential, erythroid, and granulocyte/macrophage (GM) progenitor cells, including those with high proliferative potential, was obtained without prestimulation with growth factors, indicating that these immature and mature hematopoietic progenitor cells were susceptible to infection by the recombinant AAV virions. Successful transduction did not require and was not enhanced by prestimulation of these cell populations with cytokines. The functional activity of the transduced neo gene was evident by the development of resistance to the drug G418, a neomycin analogue. Individual high and low proliferative colony-forming unit (CFU)-GM, burst-forming unit-erythroid, and CFU- granulocyte erythroid macrophage megakaryocyte colonies from mock- infected, or the recombinant virus-infected cultures were subjected to polymerase chain reaction analysis using a neo-specific synthetic oligonucleotide primer pair. A 276-bp DNA fragment that hybridized with a neo-specific DNA probe on Southern blots was only detected in those colonies cloned from the recombinant virus-infected cells, indicating stable integration of the transduced neo gene. These studies suggest that parvovirus-based vectors may prove to be a useful alternative to the more commonly used retroviral vectors for high efficiency gene transfer into slow or noncycling primitive hematopoietic progenitor cells, without the need for growth factor stimulation, which could potentially lead to differentiation of these cells before transplantation.
Eye-head coordination during head-unrestrained gaze shifts in rhesus monkeys.

We analyzed gaze shifts made by trained rhesus monkeys with completely unrestrained heads during performance of a delayed gaze shift task. Subjects made horizontal, vertical, and oblique gaze shifts to visual targets. We found that coordinated eye-head movements are characterized by a set of lawful relationships, and that the initial position of the eyes in the orbits and the direction of the gaze shift are two factors that influence these relationships. Head movements did not contribute to the change in gaze position during small gaze shifts (<20 degrees) directed along the horizontal meridian, when the eyes were initially centered in the orbits. For larger gaze shifts (25-90 degrees), the head contribution to the gaze shift increased linearly with increasing gaze shift amplitude, and eye movement amplitude saturated at an asymptotic amplitude of approximately 35 degrees. When the eyes began deviated in the orbits contralateral to the direction of the ensuing gaze shift, the head contributed less and the eyes more to amplitude-matched gaze shifts. The relative timing of eye and head movements was altered by initial eye position; head latency relative to gaze onset increased as the eyes began in more contralateral initial positions. The direction of the gaze shift also affected the relative amplitudes of eye and head movements; as gaze shifts were made in progressively more vertical directions, eye amplitude increased and head contribution declined systematically. Eye velocity was a saturating function of gaze amplitude for movements without a head contribution (gaze amplitude <20 degrees). As head contribution increased with increasing gaze amplitude (20-60 degrees), peak eye velocity declined by >200 degrees/s and head velocity increased by 100 degrees/s. For constant-amplitude eye movements (approximately 30 degrees), eye velocity declined as the velocity of the concurrent head movement increased. On the basis of these relationships, it is possible to accurately predict gaze amplitude, the amplitudes of the eye and head components of the gaze shift, and gaze, eye, and head velocities, durations and latencies if the two-dimensional displacement of the target and the initial position of the eyes in the orbits are known. These data indicate that signals related to the initial positions of the eyes in the orbits and the direction of the gaze shift influence separate eye and head movement commands. The hypothesis that this divergence of eye and head commands occurs downstream from the superior colliculus is supported by recent electrical stimulation and single-unit recording data.
Distribution of alpha-amino-3-hydroxy-5-methyl-4 isoazolepropionic acid and N-methyl-D-aspartate receptor subunits in the vestibular and spiral ganglia of the mouse during early development.

We investigated the distribution of the glutamate receptor subunits, alpha-amino-3-hydroxy-5-methyl-4 isoazolepropionic acid (AMPA) GluR2 and GluR2/R3, and N-methyl-D-aspartate (NMDA) NR1, and the timing of their appearance during early development of the mouse vestibular and spiral ganglia. NMDA NR1 was the first to be expressed, in the statoacoustic ganglion neurons on E11. GluR2/R3 immunoreactivity was detected in these neurons on E12. This signal probably corresponded exclusively to GluR3, as no signal was obtained for GluR2 alone at this stage. The appearance of these proteins began much earlier than previously reported. GluR2 staining was observed later, on E14 in the vestibular neurons and on E17 in the spiral neurons. The sequence in which these three glutamate receptors appeared suggested possible differences in their roles in the establishment of neuronal circuitry in the inner ear sensory epithelia. The production of NR1 and GluR2/R3 began during the early period of neuron growth and fasciculation. GluR2 appeared later and its expression paralleled synaptogenesis in the vestibular sensory epithelia and in the organ of Corti.
Investigating the Suitability of a Software Capture Trigger in a 3D Reconstruction System for Telepresence

In this paper we examine how closely together images to be used in 3D reconstruction are captured, when acquisition is started using a software-based trigger delivered to multiple computers on a network. In addition we compare a software triggered pull system to a push system. Synchronisation is a key component in 3D reconstruction systems and can also be one of the most problematic. In a shape-from-silhouette based system, images are captured at the same moment to ensure the position of the object is consistent in all frames. Differences in position between captured frames results in deformations such as holes and missing or extended features. By capturing images of a projected clock, we can tell with around 10ms granularity, how closely together images are captured. This gives us an indication of whether software capture triggers delivered over a network can be used for image acquisition in a 3D reconstruction system, instead of hardware synchronised capture.
On the impossibility of approximate obfuscation and applications to resettable cryptography

The traditional notion of program obfuscation requires that an obfuscation ~Prog of a program Prog computes the exact same function as Prog, but beyond that, the code of ~Prog should not leak any information about Prog. This strong notion of virtual black-box security was shown by Barak et al. (CRYPTO 2001) to be impossible to achieve, for certain unobfuscatable function families. The same work raised the question of approximate obfuscation, where the obfuscated ~Prog is only required to approximate Prog; that is, ~Prog only agrees with Prog with high enough probability on some input distribution. We show that, assuming trapdoor permutations, there exist families of robust unobfuscatable functions for which even approximate obfuscation is impossible. Specifically, obfuscation is impossible even if the obfuscated ~Prog is only required to agree with Prog with probability slightly more than 1/2, on a uniformly sampled input (below 1/2-agreement, the function obfuscated by ~Prog is not uniquely defined). Additionally, assuming only one-way functions, we rule out approximate obfuscation where ~Prog may output bot with probability close to $1$, but otherwise must agree with Prog. We demonstrate the power of robust unobfuscatable functions by exhibiting new implications to resettable protocols. Concretely, we reduce the assumptions required for resettably-sound zero-knowledge to one-way functions, as well as reduce round-complexity. We also present a new simplified construction of a simultaneously-resettable zero-knowledge protocol. Finally, we construct a three-message simultaneously-resettable witness-indistinguishable argument of knowledge (with a non-black-box knowledge extractor). Our constructions use a new non-black-box simulation technique that is based on a special kind of "resettable slots". These slots are useful for a non-black-box simulator, but not for a resetting prover.
On the display of haptic recordings for cutting biological tissues

Current simulations of surgical procedures do not provide haptic feedback of cutting forces felt while using surgical scissors. We have designed and tested "haptic scissors," an interface that can display forces to a user grasping Metzenbaum scissor handles. By, filtering and scaling cutting data obtained in previous work, we have created haptic virtual environments that can simulate the cutting of rat skin, liver, and tendon, as well as empty scissors. Preliminary perceptual experiments showed that the users rank the stiffness of real and virtual tissues similarly. Tests also demonstrated that users are not generally adept at identifying tissue types by haptic feedback in either real or virtual domains. The use of "haptic recordings," rather than reality-based models, was simple and computationally efficient. However, the simulations lack flexibility because only the exact information obtained during data acquisition can be displayed.
How Persistent and General Is the Contextual Interference Effect?

The persistence and generality of the contextual interference (CI) effect was tested using a rapid sequential aiming task. Participants (N = 48) practiced three movement patterns for three blocks of 18 trials under a blocked (BL) or random (RA) schedule. Movement patterns were displayed and KR provided throughout practice and testing. A 24-hr delayed knowledge of results (KR) retention test included three blocks of 18 trials, followed by a transfer test of a single new movement pattern. In contradiction of the CI effect, RA practice provided an advantage for RA retention only, not BL retention. Furthermore, group differences at transfer were not persistent. Hence, RA practice does not necessarily provide enhanced, context-free learning, but it is essential training for task switching. Overall the findings reveal limited persistence and generality of the CI effect.
Introduction to Clustering Large and High-Dimensional Data

1. Introduction and motivation 2. Quadratic k-means algorithm 3. BIRCH 4. Spherical k-means algorithm 5. Linear algebra techniques 6. Information-theoretic clustering 7. Clustering with optimization techniques 8. k-means clustering with divergence 9. Assessment of clustering results 10. Appendix: Optimization and Linear Algebra Background 11. Solutions to selected problems.
Measurement of HE4 and CA125 and establishment of reference intervals for the ROMA index in the sera of pregnant women

Cancer antigen 125 (CA125) and human epididymis protein 4 (HE4) are biomarkers for ovarian cancer. Their specificity and sensitivity are often limited during pregnancy as a result of great fluctuations. The risk of ovarian malignancy algorithm (ROMA) score, which combines CA125, HE4, and menopausal status, may improve diagnostic performance. There are no reports regarding the ROMA index in pregnant women. Therefore, the aim of our study was to establish appropriate reference intervals (RIs) for the ROMA index in pregnant Chinese women and compare them with those of CA125 and HE4 during pregnancy.
ABO-Incompatible Kidney Transplantation

ABO-incompatible (ABOi) kidney transplantation has long been considered a contraindication to successful kidney transplantation. During the last 25 years, increasing organ shortage enforced the development of strategies to overcome the ABO antibody barrier. In the meantime, ABOi kidney transplantation has become a routine procedure with death-censored graft survival rates comparable to the rates in compatible transplantations. Desensitization is usually achieved by apheresis and B cell-depleting therapies that are accompanied by powerful immunosuppression. Anti-A/B antibodies are aimed to be below a certain threshold at the time of ABOi kidney transplantation and during the first 2 weeks after surgery. Thereafter, even a rebound of anti-A/B antibodies does not appear to harm the kidney transplant, a phenomenon that is called accommodation, but is poorly understood. There is still concern, however, that infectious complications such as viral disease, Pneumocystis jirovecii pneumonia, and severe urinary tract infections are increased after ABOi transplantations. Recent data from the Collaborative Transplant Study show that during the first year after kidney transplantation, one additional patient death from an infectious complication occurs in 100 ABOi kidney transplant recipients. Herein, we review the recent evidence on ABOi kidney transplantation with a focus on desensitization strategies and respective outcomes.
Structure of the vertical and horizontal system neurons of the lobula plate in Drosophila

The lobula plate in the optic lobe of the fly brain is a high‐order processing center for visual information. Within the lobula plate lie a small number of giant neurons that are responsible for the detection of wide field visual motion. Although the structure and motion sensitivity of these cells have been extensively described in large flies, the system has not been described systematically in Drosophila. Here, we use the mosaic analysis with a repressible cell marker (MARCM) system to analyze a subset of these cells, the horizontal and vertical systems. Our results suggest that the Drosophila horizontal system is similar to those described in larger flies, with three neurons fanning their dendrites over the lobula plate. We found that there are six neurons in the Drosophila vertical system, a figure that compares with 9–11 neurons in large flies. Even so, the Drosophila vertical system closely resembles the systems of larger flies, with each neuron in Drosophila having an approximate counterpart in large flies. This anatomical similarity implies that the inputs to the vertical system are similarly organized in these various fly species, and that it is likely that the Drosophila neurons respond to motions similar to those sensed by their specific structural counterparts in large flies. Additionally, the similar appearance of vertical system cells in multiple cell clones demonstrates that they share a common developmental lineage. Access to these cells in Drosophila should allow for the use of genetic tools in future studies of horizontal and vertical system function. J. Comp. Neurol. 454:470–481, 2002. © 2002 Wiley‐Liss, Inc.