Miracle-dz/UniFAR-FTUs huggingface dataset:
Arrangement of photosystem II supercomplexes in crystalline macrodomains within the thylakoid membrane of green plant chloroplasts.

The chloroplast thylakoid membrane of green plants is organized in stacked grana membranes and unstacked stroma membranes. We investigated the structural organization of Photosystem II (PSII) in paired grana membrane fragments by transmission electron microscopy. The membrane fragments were obtained by a short treatment of thylakoid membranes with the mild detergent n-dodecyl-alpha, d-maltoside and are thought to reflect the grana membranes in a native state. The membranes frequently show crystalline macrodomains in which PSII is organized in rows spaced by either 26.3 nm (large-spaced crystals) or 23 nm (small-spaced crystals). The small-spaced crystals are less common but better ordered. Image analysis of the crystals by an aperiodic approach revealed the precise positions of the core parts of PSII in the lattices, as well as features of the peripheral light-harvesting antenna. Together, they indicate that the so-called C(2)S(2) and C(2)S(2)M supercomplexes form the basic motifs of the small-spaced and large-spaced crystals, respectively. An analysis of a pair of membranes with a well-ordered large-spaced crystal reveals that many PSII complexes in one layer face only light-harvesting complexes (LHCII) in the other layer. The implications of this type of organization for the efficient transfer of excitation energy from LHCII to PSII and for the stacking of grana membranes are discussed.
Peroneal bypass is equivalent to inframalleolar bypass for ischemic pedal gangrene.

OBJECTIVE To determine if peroneal bypass is a suitable alternative to inframalleolar bypass in patients with ischemic pedal gangrene. DESIGN Review of a prospectively acquired vascular registry. SETTING University practice limited to vascular surgery. PATIENTS Patients with chronic lower-extremity ischemia and pedal gangrene evaluated between 1985 and 1995 in whom the only options for arterial reconstruction were bypass to the peroneal or an inframalleolar artery. INTERVENTIONS Peroneal or inframalleolar reverse vein bypass. MAIN OUTCOME MEASURES Time to healing and lifetable analyses of survival, primary patency, and limb salvage. RESULTS Eighty-three peroneal and 46 pedal bypasses were performed for ischemic foot gangrene. The groups were equivalent for sex, diabetes mellitus, heart disease, hypertension, renal failure, hypercoagulable states, previous ipsilateral bypass, smoking, and preoperative ankle-brachial indices. Patients with inframalleolar bypass were younger than patients with peroneal bypass (63.9 vs 71.6 years, P = .005) and had higher postoperative ankle-brachial indices (1.02 vs 0.91, P = .004). However, 3-year survival rates (69.1% inframalleolar vs 60.0% peroneal, P = .35), limb salvage rates at 2 years (70.3% vs 85.8%, P = .10), and time to wound healing (19.7 vs 21.6 weeks, P = .66) were equivalent. CONCLUSION Peroneal and inframalleolar bypass for ischemic pedal gangrene have equivalent intermediate-term survival, limb salvage, and wound healing. Surgeons should not feel obliged to perform inframalleolar bypass for pedal gangrene if peroneal bypass is possible.
Low‐Frequency Earthquakes and Pore Pressure Transients in Subduction Zones

Low‐frequency earthquakes (LFEs) have been observed in subduction zones and some major tectonic faults and may well be the most important constituents of tectonic tremors. In subduction zones, they were initially attributed to fluids released by dehydration reactions in downgoing slabs. Their seismic radiation pattern, however, is consistent with shear slip on the subduction interface, and this rapidly became the favored model. Recent studies indicate that the source duration of LFEs does not scale with magnitude, which can hardly be explained by shear rupture. We revisit the characteristics of LFE events in subduction zones as retrieved from local seismic arrays. We demonstrate that they can be explained equally well by forces acting in the direction of fluid motion. Such forces may be generated by a fast local pressure variations associated with unsteady fluid motion. The amount of fluid required for LFE activity is consistent with dehydration reaction rates.
Intranasal immunization of mice with Echinococcus granulosus surface antigens Iscoms evokes a strong immune response, biased towards glucidic epitopes

The present work describes the preparation and characterization of iscoms from tegumental antigens of Echinococcus granulosus protoscoleces, and their use as immunogens in mice by intranasal and subcutaneous routes. Iscoms given at 10 mg doses evoke a significant antibody response when administered i.n. and a strong and long lasting antibody response by s.c. route. The Ag administered i.n. in a non‐adjuvanted form as a booster was not immunogenic. The i.n. route of immunization induced higher IgA serum titre in relation to IgG than the s.c. route and antisera of slightly higher avidity. Also, ten fold lower IgG2a/IgG1 and ten fold higher IgG3/IgG1 ratios were observed for the i.n. protocol compared to the s.c. one. Moreover, the mucosal route of immunization induced more efficiently antibodies of both isotypes directed to carbohydrate epitopes. The differences between immune response generated by i.n. and parenteral immunizations should be taken into consideration, particularly in those cases in which protective antigens are glycosylated.
A fast algorithm for speech polarity detection using long-term linear prediction

Speech polarity detection is a crucial first step in many speech processing techniques. In this paper, an algorithm is proposed that improvises the existing technique using the skewness of the voice source (VS) signal. Here, the integrated linear prediction residual (ILPR) is used as the VS estimate, which is obtained using linear prediction on long-term frames of the low-pass filtered speech signal. This excludes the unvoiced regions from analysis and also reduces the computation. Further, a modified skewness measure is proposed for decision, which also considers the magnitude of the skewness of the ILPR along with its sign. With the detection error rate (DER) as the performance metric, the algorithm is tested on 8 large databases and its performance (DER=0.20%) is found to be comparable to that of the best technique (DER=0.06%) on both clean and noisy speech. Further, the proposed method is found to be ten times faster than the best technique.
Differentiation and interaction of secretory immunoglobulin A and a calcium-dependent parotid agglutinin for several bacterial strains

Previous studies have suggested that both secretory immunoglobulin A (sIgA) and various nonimmunoglobulin salivary glycoproteins are capable of agglutinating a variety of bacteria. The present study was designed to compare the nature of the agglutinins for Streptococcus mutans and Salmonella typhimurium in parotid saliva and colostrum. S. mutans was aggregated by saliva and colostrum, whereas S. typhimurium was aggregated only by saliva as detected by a spectrophotometric method. The principal salivary agglutinin for both S. mutans and S. typhimurium was calcium dependent and could be desorbed in phosphate-buffered saline (pH 6.8). In contrast, the colostral agglutinin was calcium independent and not readily desorbed. The agglutinin activities of saliva and colostrum for S. mutans were additive, suggesting independent target sites on the bacterial surface. The agglutinin activity of colostrum was totally associated with sIgA as was suggested by blocking of the agglutinating activity with anti-alpha-chain serum and the absence of blocking with an antibody specific for salivary agglutinin. Interestingly, anti-alpha-chain serum removed all agglutinating activity from saliva, but not from the phosphate-buffered saline-desorbed agglutinin. Dialysis of parotid saliva against 0.1 M disodium EDTA eliminated the agglutinin blocking activity of anti-alpha-chain serum but not that of the antiagglutinin antibody. The ability of anti-alpha-chain serum to block agglutination of the EDTA-dialyzed saliva could be restored by the addition of calcium chloride, suggesting that sIgA and salivary agglutinin are associated through a calcium-mediated interaction. These results indicate that bacterial agglutinating activity of colostrum, as detected spectrophotometrically, is mediated by sIgA, and that of saliva is mainly dependent upon a calcium-dependent nonimmunoglobulin agglutinin. The agglutinating activities of sIgA and parotid agglutinin seem to be additive, and their calcium-dependent association may favor the enhancement of their respective activities.
SNPedia: a wiki supporting personal genome annotation, interpretation and analysis

SNPedia (http://www.SNPedia.com) is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Online since 2006 and freely available for personal use, SNPedia has focused on the medical, phenotypic and genealogical associations of single nucleotide polymorphisms. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). In this article, we discuss the growth of this resource and its use by affiliated software to create personal genome reports.
openSNP–A Crowdsourced Web Resource for Personal Genomics

Genome-Wide Association Studies are widely used to correlate phenotypic traits with genetic variants. These studies usually compare the genetic variation between two groups to single out certain Single Nucleotide Polymorphisms (SNPs) that are linked to a phenotypic variation in one of the groups. However, it is necessary to have a large enough sample size to find statistically significant correlations. Direct-To-Consumer (DTC) genetic testing can supply additional data: DTC-companies offer the analysis of a large amount of SNPs for an individual at low cost without the need to consult a physician or geneticist. Over 100,000 people have already been genotyped through Direct-To-Consumer genetic testing companies. However, this data is not public for a variety of reasons and thus cannot be used in research. It seems reasonable to create a central open data repository for such data. Here we present the web platform openSNP, an open database which allows participants of Direct-To-Consumer genetic testing to publish their genetic data at no cost along with phenotypic information. Through this crowdsourced effort of collecting genetic and phenotypic information, openSNP has become a resource for a wide area of studies, including Genome-Wide Association Studies. openSNP is hosted at http://www.opensnp. org, and the code is released under MIT-license at http://github.com/gedankenstuecke/snpr.
Primary intravascular large B-cell lymphoma of the lung: a review and case report.

OBJECTIVE To investigate the clinicopathological features of primary intravascular large B-cell lymphoma (IVLBCL) of the lung. METHODS Histopathological and clinical data based on lung biopsy were analyzed and used to diagnose a patient with IVLBCL of the lung. RESULTS Fever and respiratory symptoms were the main presentations, lung biopsy revealed lymphoma cells in the lumen of small blood vessels. Tumor cells expressed Bcl-2, the Bcl-6, CD20, Ki67, MUM-1, Pax5, CD, CD30, and vascular endothelial CD34. CONCLUSIONS Primary pulmonary IVLBCL of the lung is extremely rare, on chest CT it manifests as diffuse ground glass shadow, or nodular consolidations in the lung, lactate dehydrogenase and C-reactive protein was found to increase, fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) is an important and significant diagnostic modality in its early diagnosis. Also, bronchial lung biopsy has the advantage of less trauma and high sensitive rate. R-CHOP is the main treatment for lung primary pulmonary IVLBCL of the lung; however, its prognosis is relatively poor.
Predicting root biomass from branching patterns of Douglas-fir root systems

There are many examples of branching networks in nature, such as tree crowns, river systems, arteries and lungs. These networks have often been described as being self-similar, or following scale-invariant branching rules, and this property has been used to derive several scaling laws. In this paper we model root systems of Douglas-fir (Pseudotsuga menziesii var. glauca (Beissn.) Franco) as branching networks following several simple branching rules. Our objective is to establish a relationship between trunk diameter and root biomass. We explore the effect of the self-similar branching assumption on this relationship. Using data collected from a mature stand in British Columbia, we find that branching asymmetry and the rate of root taper change with root size, thereby violating the assumption of self-similarity. However, the data are in general agreement with Leonardo da Vinci's area-preserving branching hypothesis. We use the field data to parameterize two models, one assuming self-similar branching and a second incorporating the measured size dependencies of branching parameters. The two models differ by only a small amount (≈8%) in their predictions. For both models, the predicted relationship between trunk diameter and root biomass is in good concordance with previously published empirical data. We conclude that the assumption of self-similar branching, although violated by the data, nevertheless provides a useful tool for predicting the allometric relationship between trunk diameter and root biomass. Finally, we use our models to show that the geometric properties of individual bifurcations fundamentally change the root biomass cost of different root topologies.
Ostracoda from the upper Jurassic Cotton Valley group of Louisiana and Arkansas

Seven new ostracode species belonging to the new genera Schuleridea and Paraschuleridea and a new species of Brachycythere are described from the Cotton Valley group of the subsurface Upper Jurassic deposits of Louisiana and Arkansas. A ninth species is provisionally referred to Cypridea wyomingensis.
Managing inconsistencies in an evolving specification

In an evolving specification, considerable effort is spent handling recurrent inconsistencies. Detecting and resolving inconsistencies is only part of the problem: a resolved inconsistency might not stay resolved. Frameworks in which inconsistency is tolerated help by allowing resolution to be delayed. However, evolution of a specification may affect both resolved and unresolved inconsistencies. We address these problems by explicitly recording relationships between partial specifications (ViewPoints), representing both resolved and unresolved inconsistencies. We assume that ViewPoints will often be inconsistent with one another, and we ensure that a complete work record is kept, detailing any inconsistencies that have been detected, and what actions, if any, have been taken to resolve them. The work record is then used to reason about the effects of subsequent changes to ViewPoints, without constraining the development process.
Adenoviral Vector as a Gene Delivery System into Cultured Rat Neuronal and Glial Cells

Previous studies have demonstrated that a defective recombinant adenovirus can infect a wide range of postmitotic and slowly proliferating cell types such as hepatocytes, myotubes, pneumocytes and intestinal cells (Stratford‐Perricaudet et al., Hum. Gene Ther., 1, 241–256, 1990; Quantin et al., Proc. Natl. Acad. Sci. USA, 89, 2581–2584, 1992; Jaffe et al., Nature Genetics, 1, 372–378, 1992). We have used a defective recombinant adenovirus, Ad. RSVβgal, containing the Escherichia coliβ‐galactosidase gene targeted to the nucleus under the transcriptional control of the Rous sarcoma virus long terminal repeat promoter (Stratford‐Perricaudet et al., J. Clin. Invest., 90, 626–630, 1992) to infect non‐dividing neural cells in primary culture. We show that 80–100% of neuronal and astroglial cells infected with a viral titre lower than 109 p.f. u. /ml express β‐galactosidase for at least 1 month without cell damage. These results demonstrate the potential usefulness of recombinant adenovirus infection for the analysis of brain‐specific gene regulation and for the transfer of genes into neural cells before their transplantation into the brain.
Optimization of Principal-Component-Analysis-Applied in Situ Spectroscopy Data Using Neural Networks and Genetic Algorithms

A new model of multidimensional in situ diagnostic data is presented. This was accomplished by combining a back-propagation neural network (BPNN), principal component analysis (PCA), and a genetic algorithm (GA). The PCA was used to reduce input dimensionality. The GA was applied to search for a set of optimized training factors involved in BPNN training. The presented technique was evaluated with optical emission spectroscopy (OES) data measured during the etching of oxide thin films in a CHF3–CF4 inductively coupled plasma. For a systematic modeling, the etching process was characterized by a face-centered Box Wilson experiment. The etch responses to be modeled include oxide etch rate, oxide profile angle, and oxide etch rate non-uniformity. In PCA, three types of data variances were employed and the reduced input dimensionality corresponding to 100, 99, and 98% are 16, 8, and 5. The BPNN training factors to be optimized include the training tolerance, number of hidden neurons, magnitude of initial weight distribution, gradient of bipolar sigmoid function, and gradient of linear function. The prediction errors of GA-BPNN models are 249 Å/min, 2.64°, and 0.439% for the etch rate, profile angle, and etch rate non-uniformity, respectively. Compared to the conventional and previous full OES models, the presented models demonstrated a significantly improved prediction for all etch responses.
Segmented addressable scan architecture

This paper presents a test architecture that addresses multiple problems faced in digital IC testing. These problems are test data volume, test application time, test power consumption, and tester channel requirements. With minimal hardware overhead, the architecture provides at least an order of magnitude reduction to each of the above problems. The architecture relies on scan chain segmentation and multiple-hot decoders.
Basal-like breast carcinoma: from expression profiling to routine practice.

CONTEXT Advances in the understanding of the molecular and genetic mechanisms of breast cancer have led to realization of the heterogeneity of the disease and the promise of a new era of individualized management for patients with breast cancer. The advent and use of high-throughput molecular methods for the study of breast cancer have brought to the forefront the existence of the so-called basal-like breast cancers, which have been shown to have distinct biologic and clinical characteristics. OBJECTIVE To critically assess the clinicopathologic features of basal-like breast cancer, discuss the morphologic and immunophenotypic features of basal-like cancer, and explore the criteria that can be used to identify these tumors in routine practice. DATA SOURCES A Medline/PubMed search was conducted using the terms "basal-like," "(basal OR basaloid OR basal-like) AND breast cancer. " All articles in English language were retrieved and critically reviewed. CONCLUSIONS Basal-like breast cancers constitute a distinct, yet heterogeneous, class of neoplasms associated with specific histologic features and poor prognosis despite high response rates to neoadjuvant chemotherapy. Basal-like breast cancers have features that recapitulate those of tumors arising in BRCA1 mutation carriers, and the majority of patients with BRCA1 germline mutations develop basal-like breast cancers. At the molecular level, basal-like cancers harbor a transcriptome that is distinct from that of hormone-receptor-positive or HER2-amplified tumors, being characterized by the expression of genes usually found in basal/myoepithelial cells of the breast. However, translating the new concepts about basal-like cancer into clinical practice has proven a Herculean task, given the lack of an internationally accepted definition for these tumors and for the method of identification in routine practice.
Maritime Traffic Analysis of the Strait of Istanbul based on AIS data

The Strait of Istanbul is one of the most congested and risky waterways in the world. Navigation patterns have been investigated using Automatic Indentification System (AIS) data collected over a long period. 1·5 billion AIS messages, gathered over a year from 309,000 moving vessels in the Strait were stored in a Structured Query Language (SQL) database. Grid-based analysis is used to track the time, number, position, type, dimension, heading, speed and course over ground of ships. Local traffic, whose effect on maritime risk has often been neglected, is found to dominate transit traffic by a ratio of eight to one. Vessel distributions indicate that the most common lengths of vessels are 100 m and 170 m. Draught analysis shows a net transfer of goods from north to south. Southbound vessels are more likely to exceed the enforced speed limit due to predominant currents. Courses indicate that the local traffic strongly affects navigation patterns, especially at sectors with sharp turns. All these results help to understand the navigation patterns of ships and give the necessary input to assist in predicting maritime risk.
Retinomotor and Diurnal Rhythm in Crustaceans

The demonstration of the existence of a diurnal rhythm in the migration of the pigment in Leanab, Portunus, Pachygrapsus and Careinus justifies the supposition that in many species of Crustaceans such a rhythm exists in the retinomotor changes of one of the pigment systems. These periodic changes in the position of the pigment, despite the exclusion of all light, correspond with sunrise and sunset. Even if the animal is kept in complete darkness during the hours of daytime, the pigment systems concerned exhibit a partial migration towards the position of light-adaptation; when the night returns the pigment system resumes its maximum state of dark-adaptation and is found in the same position as in the previous night. The measurement of the size of the pseudo-pupil is of value in proving, in vivo , the existence of a diurnal rhythm in the iris pigment. The existence of a periodic change in the luminosity of the living eye when examined with the ophthalmoscope is of no value in ascertaining the occurrence of a diurnal rhythm in the retinal pigment or in the tapetum. In C. maenas it was possible to demonstrate a periodic variation in metabolism, in terms of a diurnal rhythm in the production of carbon dioxide. This production was about 30 % smaller during the day than during the night. The diurnal retinomotor rhythm may depend on a periodic hypoxaemia of the cell systems concerned.