Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered gene expression in the eye of a mouse model for batten disease.

PURPOSE Juvenile neuronal ceroid lipofuscinosis (JNCL or Batten Disease) is one of the most common progressive neurodegenerative disorders of childhood, resulting from autosomal recessive inheritance of mutations in the CLN3 gene. Pathologically, Batten disease is characterized by lysosomal storage of autofluorescent material in all tissue types. Although characterized by seizures, mental retardation, and loss of motor skills, the first presenting symptom of Batten disease is vision loss. METHODS High-density oligonucleotide arrays were used to profile approximately 19,000 mRNAs in the eye of 10-week-old Cln3-knockout and normal mice, and the data were compared with that for the cerebellum in the same model as a means to identify gene expression changes that are specific to the eye. RESULTS A detailed list was compiled of 285 functionally categorized genes that have altered expression in the eye of Cln3-knockout mice before the appearance of the characteristic lysosomal storage material. Furthermore, 18 genes were identified and 6 validated by semiquantitative RT-PCR that have altered expression in the eye, but not in the cerebellum of Cln3-knockout mice. The genes that have altered expression specific to the eye of the Cln3-knockout mouse may be of importance in understanding the function of CLN3 in different tissues. CONCLUSIONS Downregulation of genes associated with energy production in the mitochondria appears to be specific to the eye. The CLN3 defect may result in altered mitochondrial function in eye but not other tissue. More detailed experimentation is needed to understand the contribution of these changes in expression to disease state, and whether these changes are specific for certain cell types within the eye.
Treatment of Constipation with High‐bran Bread in Long‐term Care of Severely Demented Elderly Patients

Constipation in institutionalized elderly is a common and difficult problem. Thirty‐three institutionalized demented patients with severe constipation were given a high‐bran bread instead of their accustomed laxatives. Changes in defecation habits, food and liquid intake, and metabolic status were registered. During the high‐bran bread treatment period, the number of bowel evacuations and the estimated volume of feces increased. The total laxative consumption (doses given per day) decreased by 93 per cent. Nutritional data and metabolic status were unchanged during the high‐bran bread period except for a reduction of the postprandial blood glucose response after the glucose tolerance test.
Malignant Odontogenic Tumors: A 22‐Year Experience

Objectives/Hypothesis: Malignant odontogenic tumors are exceedingly rare and arise from odontogenic epithelial residues and odontogenic cysts in the jaw bones. Odontogenic malignancies have various origins. Some develop directly from the remnants of odontogenic epithelium left after completion of dental development; others may result from malignant transformation of a benign odontogenic cyst or ameloblastoma. These lesions are usually locally aggressive with radical surgery being the primary mode of treatment. Because of their rarity, much of the existing information about malignant odontogenic tumors with regard to their origin, clinicopathological features, biological behavior, and therapeutics is derived from case reports or small series. The study represents one of the largest series of malignant odontogenic tumors compiled in a single institution.
Association of Freestanding Dialysis Facility Size, Quality Incentive Program Scores and Patient Survival

Background In 2011, The Centers for Medicare and Medicaid Services (CMS) has introduced a bundled payment reform along with a Quality Incentive Program (QIP) to bring efficiency in End stage renal disease (ESRD) care. The QIP rates facilities using clinical and reporting criteria, but misses out on patient outcomes. It penalizes facilities not achieving a target score by 0-2% of payments. The small facilities are expected to be impacted more by a reduction in payments. We determined the association between ESRD facility size and QIP scores and the association between QIP scores and patient
The Insert Region of Rac1 Is Essential for Membrane Ruffling but Not Cellular Transformation

ABSTRACT The Rho family of Ras-related proteins, which includes Rac1, RhoA, and Cdc42, is distinguished from other members of the Ras superfamily of small GTPases in that its members possess additional sequences positioned between β-strand 5 and α-helix 4, designated the insert region. Previous studies have established the importance of an intact insert region for the transforming, but not actin cytoskeletal reorganization, activities of Cdc42 and RhoA. Similarly, the insert region was determined to be essential for Rac1-mediated mitogenesis. Additionally, an intact insert region was also determined to be required for the antiapoptotic activity of Rac1 as well as for Rac1 activation of reactive oxygen species and the NF-κB transcription factor. However, it has not been determined whether the insert region is important for Rac1-mediated growth transformation. In this study, we assessed the requirement for the insert region in Rac1 transformation and signaling in NIH 3T3 cells. Unexpectedly, we found that a mutant of constitutively activated Rac1 that lacked the insert region retained potent transforming activity. The insert region of Rac1 was dispensable for Rac1 stimulation of transcription from the cyclin D1 promoter and for activation of the c-Jun, NF-κB, and E2F-1 transcription factors but was essential for Rac1 induction of serum response factor activity. While an intact insert region was dispensable for inducing reactive oxygen species production in vivo, it was required for Rac1 induction of lamellipodia. When taken together, these results show that the insert region of Rac1 serves roles in regulating actin organization and cell growth that are distinct from those of the analogous regions of Cdc42 and RhoA and support its involvement in regulating specific downstream effector interactions.
Random Walk With Restart on Multiplex and Heterogeneous Biological Networks

Recent years have witnessed an exponential growth in the number of identified interactions between biological molecules. These interactions are usually represented as large and complex networks, calling for the development of appropriated tools to exploit the functional information they contain. Random walk with restart is the state-of-the-art guilt-by-association approach. It explores the network vicinity of gene/protein seeds to study their functions, based on the premise that nodes related to similar functions tend to lie close to each others in the networks. In the present study, we extended the random walk with restart algorithm to multiplex and heterogeneous networks. The walk can now explore different layers of physical and functional interactions between genes and proteins, such as protein-protein interactions and co-expression associations. In addition, the walk can also jump to a network containing different sets of edges and nodes, such as phenotype similarities between diseases. We devised a leave-one-out cross-validation strategy to evaluate the algorithms abilities to predict disease-associated genes. We demonstrate the increased performances of the multiplex-heterogeneous random walk with restart as compared to several random walks on monoplex or heterogeneous networks. Overall, our framework is able to leverage the different interaction sources to outperform current approaches. Finally, we applied the algorithm to predict genes candidate for being involved in the Wiedemann-Rautenstrauch syndrome, and to explore the network vicinity of the SHORT syndrome. The source code and the software are freely available at: https://github.com/alberto-valdeolivas/RWR-MH.
Adaptation of the Nitrate Reductase and Griess Reaction Methods for the Measurement of Serum Nitrate plus Nitrite Levels

Nitrite and nitrate determinations in biological fluids are increasingly being used as markers of nitric oxide production. We have modified a nitrate reductase and Griess reaction method for the measurement of serum nitrate and nitrite in ultrafiltrated samples using a microtitre plate. The recoveries of nitrate and nitrite were 95% (range = 86–113%) and 100% (range = 92–109%), respectively. The intra and inter assay coefficients of variation for nitrate plus nitrite in the concentration range 40–50μM were 9·1% and 7·8%, and in the concentration range of 2·5–10μM 23·4% and 25·5%, respectively. At its lower limit the assay is able to detect 125 pmoles of nitrate plus nitrite in 50μL of sample (2·5μmol/L). A mean serum nitrate plus nitrite level of 32·8μmol/L (SD 12·3) was measured in 24 healthy adult volunteers (12 men and 12 women), no age or sex differences were noted.
Indoor Particulate Matter < 2.5 μm in Mean Aerodynamic Diameter and Carbon Monoxide Levels During the Burning of Mosquito Coils and Their Association With Respiratory Health.

BACKGROUND An estimated 700 million people suffer from mosquito-borne diseases worldwide. Various types of mosquito repellents are widely used to prevent mosquito bites. The objectives of this study were (1) to measure the indoor levels of particulate matter < 2.5 μm in mean aerodynamic diameter (PM2.5) and carbon monoxide (CO) during the burning of mosquito coils (MCs) and study the impact of indoor ventilation patterns; and (2) to study and compare the prevalence of respiratory ailments in homes using different types of mosquito repellents. METHODS Indoor PM2.5 and CO levels were measured inside a bedroom during the burning of MCs keeping the window and/or door open/closed over a 6-h duration. A cross-sectional survey was conducted in three villages where 465 individuals were administered a questionnaire that captured demographic details, type and duration of mosquito repellents used, and prevalence of respiratory symptoms and diseases. RESULTS Fifty-three percent of the subjects burned MCs on most days of the week, and 63% did so with their doors and windows closed. Burning of MCs produced very high levels of PM2.5 (1,031 μg/m(3) mean, 1,613 μg/m(3) peak) and CO (6.50 parts per million (ppm) mean, 10.27 ppm peak) when both the door and window were closed. These levels reduced by around 50% when the window was opened and > 95% when both the window and the door were opened. The prevalence rates of respiratory symptoms and diseases were higher in subjects using MCs, although not statistically significant. Those living in smaller homes and using MCs had significantly greater morbidity. CONCLUSIONS Burning of MCs produces indoor levels of PM2.5 and CO that are higher than those reported during the burning of biomass fuels for cooking purposes and may be associated with respiratory morbidity.
Genetic Characterization of Cryptosporidium spp. among Children with Diarrhea in Tehran and Qazvin Provinces, Iran

Cryptosporidium is an intracellular apicomplexan parasite that infects a wide range of vertebrates including humans. Cryptosporidiosis is a major cause of diarrhea in children with and without human immunodeficiency virus (HIV) infection in developing countries. More recently, the molecular methods for identification of morphologically indistin- guishable species have been developed. The aim of this study was to determine the characterization of various species of this coccidian among children with diarrhea by using molecular methods. Methods: Fecal samples were collected from 1263 children with diarrhea who referred to Pediatrics Medical Centers in Qazvin and Tehran, two central provinces of Iran. Initial identification of Cryptosporidium was carried out by Zeihl-Neel- sen acid-fast staining method of stool samples. DNA was extracted from positive microscopically samples and were sub- jected to a two step nested PCR-RFLP based on SSU-rRNA gene. Results: Out of 1263 collected samples, 31 (2.5%) were found to be contained Cryptosporidium oocysts. RFLP analysis showed that 80.6% of the positive isolates were Cryptosporidium parvum, 16.1% C. hominis and 3.2% had mix infection pattern of both C. parvum and C. hominis. Conclusion: Our results showed that the zoonotic pattern of transmission is predominant and has considerable significance in epidemiology of cryptosporidiosis in the study areas.
Implementing fast and simple FEC for ultra high frequency radio

This paper describes the implementation of a fast information encoder and decoder for UHF radio considering the trade-off of speed of operation and storage space. (24, 12, 8) Golay code was implemented on an 8051 core based 8-bit microcontroller with a speed of around 60 MHz. The different available techniques to encode and decode Golay codes are discussed. A comparative study of the implementation aspects of different techniques are presented and a final solution which gives the best trade-off of speed of operation and storage space is provided.
Sarcoma metastases due to iatrogenic implantation.

AIM To demonstrate the ability of extremity soft tissue sarcomas (STSs) to implant into tissues exposed during surgery. METHODS We use two cases to illustrate that wounds created during surgery for STSs, including donor sites for skin grafts, pedicled and free flaps and blood vessels used in reconstruction, should be regarded as potential sites of quasi-local recurrence. CONCLUSIONS This report reinforces the need for meticulous surgical technique and planning of procedures to avoid contamination of clean areas that might not be included in adjuvant radiotherapy fields. The cases also highlight the pivotal importance of the correct initial management of these uncommon tumours.
Regulation of Receptor-mediated Protein Kinase C Membrane Trafficking by Autophosphorylation*

Signal transduction via protein kinase C (PKC) is closely regulated by its subcellular localization. In response to activation of cell-surface receptors, PKC is directed to the plasma membrane by two membrane-targeting domains, namely the C1 and C2 regions. This is followed by the return of the enzyme to the cytoplasm, a process shown recently to require PKC autophosphorylation (Feng, X., and Hannun, Y. A. (1998) J. Biol. Chem. 273, 26870–26874). In the present study, we examined mechanisms of translocation and reverse translocation and the role of autophosphorylation in these processes. By visualizing the trafficking of wild-type as well as mutant PKCβII in live cells, we demonstrated that in response to cell-surface receptor activation, the function of the C1 region is required but not sufficient for recruitment of the enzyme to the plasma membrane. The C2 region is also critical in anchoring the enzyme to the plasma membrane. Furthermore, the inability of a kinase-deficient PKC to undergo reverse translocation was restored by the addition of intracellular calcium chelators, suggesting a role for the C2 region in the persistent phase of translocation. On the other hand, the inability of a C2 deletion mutant (C1 region intact) to translocate in response to agonist was reversed in mutants lacking kinase activity or by mutation of the Ser660autophosphorylation site to alanine, suggesting that autophosphorylation of this site is required for opposing the action of the C2 region. Therefore, the membrane-targeting function of the C1 region is facilitated by the C2 region and appears to be opposed by autophosphorylation. Taken together, these findings provide novel evidence of the functional regulation of reversible PKC membrane localization by autophosphorylation, and they show that the dynamic translocation of PKC in response to agonists is tightly regulated in a collaborative fashion by the C1 and C2 regions in balance with the effects of autophosphorylation.
Widespread expression of the peripheral myelin protein‐22 gene (pmp22) in neural and non‐neural tissues during murine development

The gene encoding the peripheral myelin protein PMP22 is affected by various mutations in the hereditary peripheral neuropathies Charcot‐Marie‐Tooth disease type 1A (CMT1A), Déjérine‐Sottas syndrome (DSS) and hereditary neuropathy with liability to pressure palsies (HNPP). In contrast to the recent remarkable progress in the genetics of the PMP22 gene, the biological function of PMP22 remains largely unknown. In this report, we have confirmed by using in situ hybridization techniques that high levels of PMP22 niRNA are present in maturing peripheral nerves of the 2‐week‐old mouse, a finding consistent with the PNS‐specific defect observed in hereditary peripheral neuropathies. However, high levels of PMP22 transcripts were also found in the villi of the adult gut, and PMP22 expression was detected in various non‐neural tissues during embryonic mouse development. In early embryogenesis (9.5 days postconception, dpc), PMP22 RNA expression appears restricted to the epithelial ectodermal layer. During early organogenesis (11.5 dpc), particularly high levels of expression are present in the capsule surrounding the liver and in the forming gut, while low levels of PMP22 mRNA can be fund in precartilagous condensations forming the vertebrae and the ventricular layer of the myelencephalon. During midgestation development (14.5 dpc to 16.5 dpc), the number of PMP22‐positive tissues increases, and high expression is detected in several mesoderm‐derived tissues, in particular connective tissues of the face region, bones including the vertebrae, the lung mesenchym, and in muscles. In addition, high expression is also found in ectoderm‐derived tissues, especially the epithelia of the lens and the skin. These findings strongly suggest that PMP22 serves not only a PNSspecific function but is also of broader biological significance in cell proliferation and/or differentiation. ©1995 Wiley‐Liss, Inc.
Postnatal development of intestinal immune system in piglets: implications for the process of weaning

European-wide directives are in place to establish a sustainable production of pigs without using production enhancers and chemotherapeutics. Thus, an economically-viable pig production is now only possible when the physiological mechanisms of defense against pathogens and tolerance against nutrients and commensal bacteria in the intestinal immune system are taken into account. During the postnatal period the piglet is facing first the time large amounts of new antigens and at weaning a second wave of nutritional antigens is entering the intestinal tract. The appropriate devel- opment of humoral and cellular functions of the intestinal immune system is essential for optimum growth and performance of the piglets. The integrity of the intestinal surfaces is a prerequisite of intestinal immunity and tolerance. Secretory IgA serves to exclude harmful antigens from uptake. The induction of intestinal immune reactions starts with antigen presentation by professional antigen presenting cells of Peyer's patches and mesenteric lymph nodes. In addition, the intestinal lamina propria serves as a mucosal compartment for regulation of immune responses. Here especially T reg- ulatory cells (CD4 + CD25 + ) have their function for maintaining intestinal homeostasis. The network of mucosal T and B cells develops after birth in a programmed sequence; it is almost completed at week 7 after birth. Weaning is associated with changes in the regulation of the lymphoid cells in the mucosa. In small and large intestine increases in pro- and anti-inflammatory cytokines were observed after weaning in lymphocytes. Epithelial cells were studied both in intestinal samples and in vitro. Here the cytokine patterns provide evidence that weaning is inducing a transient inflammation of the mucosa. Piglets weaned under conventional conditions have a thicker mucosa than pigs weaned from isolators. Cells of isolator-reared pigs show slightly higher levels of activation markers - probably
Nucleocytoplasmic Shuttling of the Rpb4p and Rpb7p Subunits of Saccharomyces cerevisiae RNA Polymerase II by Two Pathways

ABSTRACT Rpb4p and Rpb7p are subunits of the RNA polymerase II of Saccharomyces cerevisiae that form a dissociable heterodimeric complex. Whereas the only reported function of Rpb7p is related to transcription, Rpb4p has been found to also act in mRNA export and in the major mRNA decay pathway that operates in the cytoplasm, thus raising the possibility that Rpb4p links between the nuclear and cytoplasmic processes. Here we show that both Rpb4p and Rpb7p shuttle between the nucleus and the cytoplasm. Shuttling kinetics of the two proteins are similar as long as their interaction is possible, suggesting that they shuttle as a heterodimer. Under normal conditions, shuttling of Rpb4p and Rpb7p depends on ongoing transcription. However, during severe stresses of heat shock, ethanol, and starvation, the two proteins shuttle via a transcription-independent pathway. Thus, Rpb4p and Rpb7p shuttle via two pathways, depending on environmental conditions.
Long‐term administration of the low‐dose risperidone in schizotaxia subjects

The term schizotaxia is currently defined as a syndrome of neuropsychological deficits and negative symptoms found in relatives of schizophrenic patients. The aim of this study was to assess the effect of long‐term treatment with the low‐dose risperidone on cognitive and social functioning in seven schizotaxia patients. There were four males and three females, aged between 17 and 44 years, first‐degree (four patients) or second‐degree (three patients) relatives of schizophrenic patients. Schizotaxia was recognized in them on account of neuropsychological and social function impairment. They all consented to risperidone administration, 1–2 mg/day. Duration of risperidone treatment has ranged between 3–7 years. In all subjects, the continuous treatment with risperidone brought about a marked improvement in their cognitive, social, and vocational functioning. Neuropsychological testing after 6–24 months showed significant improvement on such tests as Wisconsin Card Sorting Test (WCST), Trail Making Test (TMT), and Stroop Test. Discontinuation of treatment after 3–4 years did not cause deterioration of functioning. Copyright © 2007 John Wiley & Sons, Ltd.
Analysis and Design of Two-Dimensional Resonant-Type Composite Right/Left-Handed Transmission Lines With Compact Gain-Enhanced Resonant Antennas

A two-dimensional (2-D) resonant-type composite right/left-handed transmission line (CRLH TL) is proposed consisting of complementary split-ring resonators (CSRRs) and series capacitive gaps. For characterization and design, the circuit parameters extraction procedure for the TL element is derived, and the unique 2-D dispersion characteristics (CRLH nature) are analytically investigated and further verified by eigenmode analysis performed in HFSS and phase analysis in ADS. A good agreement of dispersion diagram is obtained between full-wave simulation and theory. To demonstrate potential applications, two types of microstrip antennas have been designed, fabricated, and measured following the design procedures that are established. In the first design, a multifrequency antenna operating at three resonant modes of n = -1, n = 0, and n = + 1 is designed by arranging a 2×2 CRLH array in a conventional patch. The frequency ratios between these modes are 1.98 and 1.15, respectively, which can be arbitrarily modulated by controlling the proportion between the CRLH section and the patch. In the second design, zeroth-order resonant antennas are researched. These antennas exhibit simultaneously a leaky-wave characteristic and an omnidirectional radiation behavior, distinguishing them significantly from any previous designs. In both cases, the antenna gain is comparable, and the cell structure is uniplanar and electrically small.