Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanical factors in the excitation of clupeid lateral lines

The excitation of lateral line sense organs (neuromasts) might be expected to depend on differences of movement between the liquid inside the main lateral line canals (the ones that contain the neuromasts) and the walls of these canals. We have investigated this net movement in relation to events in the water around fish. Liquid displacements inside a given part of a main lateral line canal of the sprat (Sprattus sprattus (L.)) are, at any one frequency, linearly related to those in the medium (sea water) adjacent to this part. For the parts of the canal system studied, and below about 80 Hz, the ratio of displacement inside the canal to that in the medium falls with frequency, i. e. the displacement inside the canal follows the velocity in the medium. Sea water displacements in a given length of a main lateral line canal system are proportional to the component of the external velocity that is parallel to the canal. For this component the ratio of displacements inside and outside the lateral line approaches unity at around 80 Hz. The behaviour of a lateral line canal is close to that of a straight capillary tube of roughly the same cross sectional area. Displacements in the canal are advanced in phase relative to those in the external medium and these phase advances are a little larger than those found in capillaries. There is very little mechanical coupling between neighbouring parts of the main canals. Since the cupulae of the neuromasts of the sprat lateral line are driven by frictional forces, the stimulus to a neuromast will (below 80 Hz) be proportional to the acceleration of the medium adjacent to the lateral line. Sprats and fish of three other species (Clupea harengus L., Hyperoplus lanceolatus (Lesauvage), and Trachurus trachurus (L.) have been shown, when suspended in sound fields emitted by pulsating and vibrating sources, to behave longitudinally as rigid bodies. Under many conditions it proved possible to calculate the longitudinal movements of fish from the differences of pressure between snout and tail. From these two kinds of result we have calculated for a variety of positions in fields around vibrating bodies the motion of a fish and the motion of the liquid in the canals and so estimated the effective stimulus to different parts of the lateral line system. When such calculations were made for a vibrating source of the dimensions of a sprat tail, and for distances comparable to the inter-fish distance within a school, we found that the patterns of net velocities at different neuromasts change dramatically with the position or angle of the fish relative to the source. We estimate that the sprat lateral line system excited in this way could detect a neighbouring fish in a school at distances of up to a few fish lengths. The sprat lateral line sensory system is well suited to giving sensory information in such activities as schooling.
Lung epithelial cell apoptosis during acute lung injury in infancy

Context: Apoptosis of lung epithelial cells is implicated in the pathogenesis of acute lung injury. Most research on this subject has focused on adults. Very little is known about a potential interaction of this process with lung development in children. Objective: To summarize the current literature on lung epithelial cell apoptosis and common causes of acute lung injury in infants and young children and to identify new areas of research. Design: A Medline-based literature search. Results and Conclusions: Few studies have focused on lung epithelial cell apoptosis during common causes of acute lung injury in children. Nevertheless, the limited literature suggests that this may be an important mechanism during respiratory distress syndrome of infants and viral respiratory tract infection. Apoptosis is an essential process during lung development and maturation. Insufficient attention has been paid to potential consequences of this for the short- and long-term outcomes of acute lung injury.
Enzymatic Properties of the Recombinant Serine-Type Carboxypeptidase OcpC, Which Is Unique to Aspergillus oryzae

Gene AO090103000153 is unique to Aspergillus oryzae RIB40 and A. flavus NRRL3357, and is speculated to encode a serine-type carboxypeptidase. In this study, we purified and characterized a heterologously expressed gene product of AO090103000153. 5′-Rapid amplification of cDNA ends indicated that the translation start site of the gene is located 1,586 bp downstream of the translation start site predicted by the genome sequencing project. The gene, starting from the revised translation start codon, termed ocpC, was transcribed constantly in A. oryzae RIB40. Purified recombinant OcpC exhibited the enzymatic properties of a serine-type carboxypeptidase. This protease was stable at temperatures below 45 °C and a low pH, and had broad substrate specificity for N-acylpeptides, but it exhibited significantly lower specific activity and a lower k cat value for substrates than previously reported serine-type carboxypeptidases from A. oryzae.
Motifs IV and V in the DEAH Box Splicing Factor Prp22 Are Important for RNA Unwinding, and Helicase-defective Prp22 Mutants Are Suppressed by Prp8*

The yeast pre-mRNA splicing factor Prp22 is a member of the DEAH box family of nucleic acid-stimulated ATPases and RNA helicases. Here we report a mutational analysis of 16 conserved residues in motifs Ia (534TQPRRVAA541), IV (695LVFLTG700), and V (757TNIAETSIT765). Mutants T757A, I764A, and T765A were lethal, and F697A cells did not grow at ≤30 °C. The mutant proteins failed to catalyze mRNA release from the spliceosome in vitro, and they were deficient for RNA unwinding. The F697A, I764A, and T765A proteins were active for ATP hydrolysis in the presence of RNA cofactor. The T757A mutant retained basal ATPase activity but was not stimulated by RNA, whereas ATP hydrolysis by T765A was strictly dependent on the RNA cofactor. Thus Thr-757 and Thr-765 in motif V link ATP hydrolysis to the RNA cofactor. To illuminate the mechanism of Prp22-catalyzed mRNA release, we performed a genetic screen to identify extragenic suppressors of the cold-sensitive growth defect of a helicase/release-defective Prp22 mutant. We identified one of the suppressors as a missense mutation of PRP8 (R1753K), a protein component of the U5 small nuclear ribonucleoprotein. We show that PRP8-R1753K suppressed multiple helicase-deficient prp22 mutations, including the lethal I764A mutation. Replacing Arg-1753 of Prp8 by either Lys, Ala, Gln, or Glu resulted in suppression of helicase-defective Prp22 mutants. Prp8-Arg1753 mutations by themselves caused temperature-sensitive growth defects in a PRP22 strain. These findings suggest a model whereby Prp22 disrupts an RNA/protein or RNA/RNA interaction in the spliceosome that is normally stabilized by Prp8.
Mutational, functional, and expression studies of the TCF4 gene in Pitt‐Hopkins syndrome

Pitt‐Hopkins syndrome is a severe congenital encephalopathy recently ascribed to de novo heterozygous TCF4 gene mutations. We report a series of 13 novel PHS cases with a TCF4 mutation and show that EEG, brain magnetic resonance imagain (MRI), and immunological investigations provide valuable additional clues to the diagnosis. We confirm a mutational hot spot in the basic domain of the E‐protein. Functional studies illustrate that heterodimerisation of mutant TCF4 proteins with a tissue‐specific transcription factor is less effective than that homodimerisation in a luciferase reporter assay. We also show that the TCF4 expression pattern in human embryonic development is widespread but not ubiquitous. In summary, we further delineate an underdiagnosed mental retardation syndrome, highlighting TCF4 function during development and facilitating diagnosis within the first year of life. Hum Mutat 0, 1–8, 2009. © 2009 Wiley‐Liss, Inc.
A loosely synchronizing asynchronous router for TDM-scheduled NOCs

This paper presents an asynchronous router design for use in time-division-multiplexed (TDM) networks-on-chip. Unlike existing synchronous, mesochronous and asynchronous router designs with similar functionality, the router is able to silently skip over cycles/TDM-slots where no traffic is scheduled and hence avoid all switching activity in the idle links and router ports. In this way switching activity is reduced to the minimum possible amount. The fact that this relaxed synchronization is sufficient to implement TDM scheduling represents a contribution at the conceptual level. The idea can only be implemented using asynchronous circuit techniques. To this end, the paper explores the use of “click-element” templates. Click-element templates use only flip-flops and conventional gates, and this greatly simplifies the design process when using conventional EDA tools and standard cell libraries. Few papers, if any, have explored this.
Performance analysis of frequent itemset finding techniques using sparse datasets

Techniques for efficient mining of frequent patterns have been studied extensively by many researchers. However, the previously proposed techniques still encounter some performance bottlenecks when mining databases with different data characteristics such as, dense vs. sparse, long vs. short patterns, memory-based vs. disk-based, etc. In this study, explored the unifying feature among the internal working of various mining techniques such as, Two-Fold Cross Validation Model, Improved Apriori, CBT-fi and Semi-Apriori. Extensive experiments had been carried out and compared using the different techniques, a tentative result reveal that Semi-Apriori outperforms in terms of execution time using hepatitis and wine datasets.
Digital breast tomosynthesis: studies of the effects of acquisition geometry on contrast-to-noise ratio and observer preference of low-contrast objects in breast phantom images

The effect of acquisition geometry in digital breast tomosynthesis was evaluated with studies of contrast-to-noise ratios (CNRs) and observer preference. Contrast-detail (CD) test objects in 5 cm thick phantoms with breast-like backgrounds were imaged. Twelve different angular acquisitions (average glandular dose for each ~1.1 mGy) were performed ranging from narrow angle 16° with 17 projection views (16d17p) to wide angle 64d17p. Focal slices of SART-reconstructed images of the CD arrays were selected for CNR computations and the reader preference study. For the latter, pairs of images obtained with different acquisition geometries were randomized and scored by 7 trained readers. The total scores for all images and readings for each acquisition geometry were compared as were the CNRs. In general, readers preferred images acquired with wide angle as opposed to narrow angle geometries. The mean percent preferred was highly correlated with tomosynthesis angle (R = 0.91). The highest scoring geometries were 60d21p (95%), 64d17p (80%), and 48d17p (72%); the lowest scoring were 16d17p (4%), 24d9p (17%) and 24d13p (33%). The measured CNRs for the various acquisitions showed much overlap but were overall highest for wide-angle acquisitions. Finally, the mean reader scores were well correlated with the mean CNRs (R = 0.83).
Efficacy of the acyclic nucleoside 9-(1,3-dihydroxy-2-propoxymethyl)guanine against primary and recrudescent genital herpes simplex virus type 2 infections in guinea pigs

The acyclic nucleoside 9-(1,3-dihydroxy-2-propoxymethyl)guanine (DHPG) was evaluated for its efficacy in protecting guinea pigs from primary and recrudescent infections of herpes simplex virus type 2. Vaginally infected guinea pigs were treated twice a day with DHPG at 25 mg/kg per dose for 3 weeks. Subcutaneous doses were started 3 h, 24 h, or 5 weeks after virus inoculation. Treatment starting at 3 or 24 h reduced the severity of the primary infection by greater than 70% when lesions were graded for 3 weeks; lesion duration was lessened by greater than 55%. For 6 weeks after treatment, the number of recrudescent lesions was reduced by greater than 60%, and the duration of the recrudescences declined by greater than 40%. When dosing was started at 3 h postinfection, 33% of the animals did not develop any sign of primary or recrudescent infection throughout the 9-week test. By comparison, all the animals treated with DHPG starting at 24 h or with saline became infected. A 3-week DHPG regimen starting 5 weeks postinfection reduced the number of animals that developed recrudescent lesions by 70%. When treatment ended, however, recrudescent episodes in the animals increased to the level of saline-treated controls.These results suggest that (i) DHPG is highly effective in reducing the severity of both primary and recrudescent lesions of herpes simplex virus type 2, (ii) early treatment of a primary infection or treatment of recrudescences reduces the incidence of recrudescences, and (iii) the drug appears to have no effect on the latent form of the virus, as the incidence of recrudescences increases when DHPG treatment is ended.
Global prevalence and incidence estimates of selected curable STDs.

OBJECTIVES To update the WHO global and regional estimates of the prevalence and incidence of syphilis, gonorrhoea, chlamydia, and trichomoniasis. METHODS Prevalence estimates for syphilis, gonorrhoea, chlamydia, and trichomoniasis were generated for each of the nine UN regions for males and females between the ages of 15 and 49 in 1995 based on an extensive review of the published and unpublished medical literature since 1985. Incidence estimates were based on the prevalence figures and adjusted to take into account the estimated average duration of infection for each disease in a particular region. The latter was assumed to depend upon a number of factors including the duration of infection in the absence of treatment, the proportion of individuals who develop symptoms, the proportion of individuals treated, and the appropriateness of treatment. RESULTS In 1995 there were over 333 million cases of the four major curable STDs in adults between the ages of 15 and 49--12 million cases of syphilis, 62 million cases of gonorrhoea, 89 million cases of chlamydia, and 170 million cases of trichomoniasis. Geographically, the vast majority of these cases were in the developing world reflecting the global population distribution. CONCLUSIONS STDs are among the most common causes of illness in the world. Estimates of the global prevalence and incidence of these infections are limited by quantity and quality of data available from the different regions of the world. Improving global STD estimates will require more well designed epidemiological studies on the prevalence and duration of infection.
Overweight and obesity as determinants of cardiovascular risk: the Framingham experience.

BACKGROUND To our knowledge, no single investigation concerning the long-term effects of overweight status on the risk for hypertension, hypercholesterolemia, diabetes mellitus, and cardiovascular sequelae has been reported. METHODS Relations between categories of body mass index (BMI), cardiovascular disease risk factors, and vascular disease end points were examined prospectively in Framingham Heart Study participants aged 35 to 75 years, who were followed up to 44 years. The primary outcome was new cardiovascular disease, which included angina pectoris, myocardial infarction, coronary heart disease, or stroke. Analyses compared overweight (BMI [calculated as weight in kilograms divided by the square of height in meters], 25.0-29.9) and obese persons (BMI > or =30) to a referent group of normal-weight persons (BMI, 18.5-24.9). RESULTS The age-adjusted relative risk (RR) for new hypertension was highly associated with overweight status (men: RR, 1.46; women: RR, 1.75). New hypercholesterolemia and diabetes mellitus were less highly associated with excess adiposity. The age-adjusted RR (confidence interval [CI]) for cardiovascular disease was increased among those who were overweight (men: 1.21 [1.05-1.40]; women: 1.20 [1.03-1.41]) and the obese (men: 1.46 [1.20-1.77]; women: 1.64 [1.37-1.98]). High population attributable risks were related to excess weight (BMI > or =25) for the outcomes hypertension (26% men; 28% women), angina pectoris (26% men; 22% women), and coronary heart disease (23% men; 15% women). CONCLUSIONS The overweight category is associated with increased relative and population attributable risk for hypertension and cardiovascular sequelae. Interventions to reduce adiposity and avoid excess weight may have large effects on the development of risk factors and cardiovascular disease at an individual and population level.
Osteoprotegerin Is a Receptor for the Cytotoxic Ligand TRAIL*

TRAIL is a tumor necrosis factor-related ligand that induces apoptosis upon binding to its death domain-containing receptors, DR4 and DR5. Two additional TRAIL receptors, TRID/DcR1 and DcR2, lack functional death domains and function as decoy receptors for TRAIL. We have identified a fifth TRAIL receptor, namely osteoprotegerin (OPG), a secreted tumor necrosis factor receptor homologue that inhibits osteoclastogenesis and increases bone density in vivo. OPG-Fc binds TRAIL with an affinity of 3.0 nm, which is slightly weaker than the interaction of TRID-Fc or DR5-Fc with TRAIL. OPG inhibits TRAIL-induced apoptosis of Jurkat cells. Conversely, TRAIL blocks the anti-osteoclastogenic activity of OPG. These data suggest potential cross-regulatory mechanisms by OPG and TRAIL.
Public health concerns of highly pathogenic avian influenza H5N1 endemicity in Africa

Highly pathogenic avian influenza virus (HPAIV) H5N1 was first officially reported in Africa in 2006; thereafter this virus has spread rapidly from Nigeria to 11 other African countries. This study was aimed at utilizing data from confirmed laboratory reports to carry out a qualitative evaluation of the factors responsible for HPAI H5N1 persistence in Africa and the public health implications; and to suggest appropriate control measures. Relevant publications were sought from data banks and repositories of FAO, OIE, WHO, and Google scholars. Substantiated data on HPAI H5N1 outbreaks in poultry in Africa and in humans across the world were mined. HPAI H5N1 affects poultry and human populations, with Egypt having highest human cases (346) globally. Nigeria had a reinfection from 2014 to 2015, with outbreaks in Côte d’Ivoire, Ghana, Niger, Nigeria, and Burkina Faso throughout 2016 unabated. The persistence of this virus in Africa is attributed to the survivability of HPAIV, ability to evolve other subtypes through genetic reassortment, poor biosecurity compliance at the live bird markets and poultry farms, husbandry methods and multispecies livestock farming, poultry vaccinations, and continuous shedding of HPAIV, transboundary transmission of HPAIV through poultry trades; and transcontinental migratory birds. There is, therefore, the need for African nations to realistically reassess their status, through regular surveillance and be transparent with HPAI H5N1 outbreak data. Also, it is important to have an understanding of HPAIV migration dynamics which will be helpful in epidemiological modeling, disease prevention, control and eradication measures.
Phosphodiesterase 7A-Deficient Mice Have Functional T Cells

Phosphodiesterases (PDEs) are enzymes which hydrolyze the cyclic nucleotide second messengers, cAMP and cGMP. In leukocytes, PDEs are responsible for depletion of cAMP which broadly suppresses cell functions and cellular responses to many activation stimuli. PDE7A has been proposed to be essential for T lymphocyte activation based on its induction during cell activation and the suppression of proliferation and IL-2 production observed following inhibition of PDE7A expression using a PDE7A antisense oligonucleotide. These observations have led to the suggestion that selective PDE7 inhibitors could be useful in the treatment of T cell-mediated autoimmune diseases. In the present report, we have used targeted gene disruption to examine the role PDE7A plays in T cell activation. In our studies, PDE7A knockout mice (PDE7A−/−) showed no deficiencies in T cell proliferation or Th1- and Th2-cytokine production driven by CD3 and CD28 costimulation. Unexpectedly, the Ab response to the T cell-dependent Ag, keyhole limpet hemocyanin, in the PDE7A−/− mice was found to be significantly elevated. The results from our studies strongly support the notion that PDE7A is not essential for T cell activation.
Basic structure of basement membranes is a fine network of “cords,” irregular anastomosing strands

A three‐dimensional network of irregular anastomosing strands, referred to as “cords,” was found to be the main component of the lamina densa of (a) common, “thin” basement membranes in tissues from diverse origins including foot pad epidermis, trachea, jejunum, seminiferous tubule and vas deferens of the rat, monkey seminiferous tubule, and mouse ciliary process, (b) a “double” basement membrane, the rat glomerular basement membrane, and (c) “thick” basement membranes including rat Reichert's membrane, mouse lens capsule and the Engelbreth‐Holm‐Swarm (EHS) tumor matrix. The average thickness of the cords was 3.2–4.8 nm, 4 nm, and 4.7–5 nm, respectively, in these three types of basement membranes. The mean diameter of the intercordal spaces, or openings of the network, averaged 14 nm with a range from 8 nm in the glomerular basement membrane to 21.9 nm in the lens capsule. After cryofixation followed by freeze substitution or freeze drying, similar cord networks were observed in all basement membranes examined which included two thin basement membranes, that of the rat epididymis and seminiferous tubules, and three thick basement membranes, that is, the lens capsule and the EHS tumor matrix of the mouse, and rat Reichert's membrane. In addition, following the co‐incubation of laminin, type IV collagen and heparan sulfate proteoglycan at 35°C, a precipitate was formed which was found to contain lamina densa‐like sheets and large semisolid masses. Both types of structures were found to be made up of a network of 3 nm wide cords, which resembled that of natural basement membranes. With the immunoperoxidase technique, these cords were stained for major basement membrane components including laminin, type IV collagen, heparan sulfate proteoglycan, entactin, and fibronectin. Ribbon‐like “double tracks” 4.5 nm in width and being distributed along cords have been identified as the form taken by heparan sulfate proteoglycan in basement membranes. Following mild plasmin treatment, most of the cord components were digested away leaving behind a network of fine filaments found to contain type IV collagen. Each cord, therefore, is organized by a type IV collagen core filament which is surrounded by a plasmin‐sensitive sheath containing other basement membrane components. Two types of minor structural components, that is, 7–10 nm wide straight “basotubules” and 3.5 nm wide particulate structures referred to as “pentosomes” were associated with cord network in some basement membranes. In summary, since a fine network of about 4 nm thick cords was always found to occupy a bulk of all basement membranes examined in tissues of a diverse origin and of different species, and also after the use of different preparative methods, such cord network is likely to be the basic structure of basement membranes. © 1994 Wiley‐Liss, Inc.