Miracle-dz/UniFAR-FTUs huggingface dataset:
The impacts of deglaciation and human activity on the taxonomic structure of prokaryotic communities in Antarctic soils on King George Island

Abstract The soil microbiome was investigated at environmentally distinct locations on King George Island in the South Shetland Islands (Antarctic Peninsula) using 16 S rRNA gene pyrosequencing. The taxonomic composition of the soil prokaryotes (bacteria and archaea) was evaluated at three sites representing human-disturbed soils (Bellingshausen Station) and soils undergoing different stages of deglaciation (fresh and old moraines located near Ecology Glacier). The taxonomic analysis revealed 20 bacterial and archaeal phyla, among which Proteobacteria (29.6%), Actinobacteria (25.3%), Bacteroidetes (15.8%), Cyanobacteria (11.2%), Acidobacteria (4.9%) and Verrucomicrobia (4.5%) comprised most of the microbiome. In a beta-diversity analysis, the samples formed separate clusters. The Bellingshausen Station samples were characterized by an increased amount of Nostoc sp. and Janibacter sp. Although the deglaciation history had less of an effect on the soil microbiome, the early stages of deglaciation (Sample 1) had a higher proportion of bacteria belonging to the families Xanthomonadaceae, Sphingomonadaceae and Nocardioidaceae, whereas the older moraines (Sample 2) were enriched with Chthoniobacteriacae and N1423WL. Solirubrobacteriales, Gaiellaceae and Chitinophagaceae bacteria were present in both stages of deglaciation, characterized by genus-level differences. Taxonomic analysis of the abundant operational taxonomic units (OTUs) revealed both endemic (Marisediminicola antarctica, Hymenobacter glaciei) and cosmopolitan bacterial species in the microbiomes.
Building and re-building the heart by cardiomyocyte proliferation

The adult human heart does not regenerate significant amounts of lost tissue after injury. Rather than making new, functional muscle, human hearts are prone to scarring and hypertrophy, which can often lead to fatal arrhythmias and heart failure. The most-cited basis of this ineffective cardiac regeneration in mammals is the low proliferative capacity of adult cardiomyocytes. However, mammalian cardiomyocytes can avidly proliferate during fetal and neonatal development, and both adult zebrafish and neonatal mice can regenerate cardiac muscle after injury, suggesting that latent regenerative potential exists. Dissecting the cellular and molecular mechanisms that promote cardiomyocyte proliferation throughout life, deciphering why proliferative capacity normally dissipates in adult mammals, and deriving means to boost this capacity are primary goals in cardiovascular research. Here, we review our current understanding of how cardiomyocyte proliferation is regulated during heart development and regeneration. Summary: This Review article discusses the cellular and molecular mechanisms that control cardiomyocyte proliferation, during both heart development and regeneration across various species.
Towards a Communication Brain Computer Interface Based on Semantic Relations

This article investigates a possible Brain Computer Interface (BCI) based on semantic relations. The BCI determines which prime word a subject has in mind by presenting probe words using an intelligent algorithm. Subjects indicate when a presented probe word is related to the prime word by a single finger tap. The detection of the neural signal associated with this movement is used by the BCI to decode the prime word. The movement detector combined both the evoked (ERP) and induced (ERD) responses elicited with the movement. Single trial movement detection had an average accuracy of 67%. The decoding of the prime word had an average accuracy of 38% when using 100 probes and 150 possible targets, and 41% after applying a dynamic stopping criterium, reducing the average number of probes to 47. The article shows that the intelligent algorithm used to present the probe words has a significantly higher performance than a random selection of probes. Simulations demonstrate that the BCI also works with larger vocabulary sizes, and the performance scales logarithmically with vocabulary size.
Inhibition of Mammalian Fertilization in Vitro by Membrane Vesicles from Seminal Plasma

Summary Vesicle fractions I and II, isolated from rabbit seminal plasma following ultracentrifugation, inhibited fertilization of rat eggs in vitro. Fertilization was reduced by 65% when the medium contained 17 μg protein/ml Fr I and by 57% when it had 5 μg protein/ml Fr. II. It was completely prevented with 83-155 and 43-85 μg protein/ml Fr I and II, respectively. Addition of 266-525 μg protein/ml whole seminal plasma or 38-175 μg protein/ml nonsedimenting seminal plasma components (Fr III) caused dissolution of the zona pellucida by constituents that were heat labile. Fertilization was inhibited by seminal plasma and promoted by Fr III. Electron micrographs of spermatozoa following incubation indicated that vesicle containing fractions from rabbit seminal plasma prevent breakdown of the plasma membrane covering the acrosome region of the head. The results are interpreted as suggesting that both classes of seminal plasma vesicles block fertilization by inhibiting sperm capacitation under defined in vitro conditions. This work was supported by N.I. H. Contract No. 1-HD-3-2781. We are grateful to Mrs. Rose Bartke and Mr. John Whitney for their skillful assistance. The electron micrographs were kindly prepared by Dr. N. Barwell, Beth Israel Hospital, Boston.
Soft Tissue Cephalometric Standards based on NHP in a Sample of Iranian Adults

Background and aims This study aimed to establish soft tissue cephalometric standards in Iranian adults based on NHP, which can be used in diagnosis of orthodontic and orthognathic patients. Materials and methods A group of 46 individuals (24 males and 22 females) with normal occlusion and proportional facial profile were chosen from a large group of dental students. For the all of the chosen sample, lateral cephalograms were obtained with head oriented in natural position. On the basis of the true horizontal and true vertical lines, the standard values of 19 soft tissue measurements were determined using McNamara, Burstone and Viazis methods. Results In this study, the mean value of SN deviation to true horizontal line was 6.6°. Comparison between two genders showed that females have more obtuse nasolabial angle and thinner soft tissue chin than males (P < 0.05). Linear measurements showed that the overall size of males was more than females (P < 0.05). Conclusion Cephalometric norms based on NHP were found to be more reliable in orthognathic pa-tients.
Low complexity hybrid precoding for mmWave Massive MIMO systems

Massive MIMO has the advantage of providing excellent multiplexing/diversity gain and data rate due to the large antenna array equipped at the BS or UEs. However, the high hardware cost and computational complexity limit the practical implementation of large antenna array. In this paper, we formulate a Minimum Mean Square Error (MMSE) based optimization model under the partially-connected structure to reduce the hardware cost, and propose a low complexity hybrid precoding algorithm based on the Particle Swarm Ant Colony Optimization (HP-PSACO). Simulation results show that the proposed algorithm with low computational complexity achieves higher energy efficiency than the fully digital baseband precoding.
A Novel Class of Anti-HIV Agents with Multiple Copies of Enfuvirtide Enhances Inhibition of Viral Replication and Cellular Transmission In Vitro

We constructed novel HIV-1 fusion inhibitors that may overcome the current limitations of enfuvirtide, the first such therapeutic in this class. The three prototypes generated by the Dock-and-Lock (DNL) technology to comprise four copies of enfuvirtide tethered site-specifically to the Fc end of different humanized monoclonal antibodies potently neutralize primary isolates (both R5-tropic and X4-tropic), as well as T-cell-adapted strains of HIV-1 in vitro. All three prototypes show EC50 values in the subnanomolar range, which are 10- to 100-fold lower than enfuvirtide and attainable whether or not the constitutive antibody targets HIV-1. The potential of such conjugates to purge latently infected cells was also demonstrated in a cell-to-cell viral inhibition assay by measuring their efficacy to inhibit the spread of HIV-1LAI from infected human peripheral blood mononuclear cells to Jurkat T cells over a period of 30 days following viral activation with 100 nM SAHA (suberoylanilide hydroxamic acid). The IgG-like half-life was not significantly different from that of the parental antibody, as shown by the mean serum concentration of one prototype in mice at 72 h. These encouraging results provide a rationale to develop further novel anti-HIV agents by coupling additional antibodies of interest with alternative HIV-inhibitors via recombinantly-produced, self-assembling, modules.
C-C chemokine receptor type 5 (CCR5) utilization of transmitted and early founder human immunodeficiency virus type 1 envelopes and sensitivity to small-molecule CCR5 inhibitors

The envelope glycoprotein (Env) of human immunodeficiency virus is key to viral entry of susceptible target cells and is therefore a major target for the design of vaccines and antiviral drugs. C-C chemokine receptor type 5 (CCR5)-using (R5) Env is the predominant phenotype associated with early transmission and acute infection. This study investigated the mechanism of CCR5 use and the sensitivity to CCR5 inhibitors of a panel of transmitted or early founder (T/F) Envs. The data showed that the majority of T/F Envs used CCR5 and that many also used CCR3, although less efficiently. Despite a similar ability to use wild-type CCR5, individual Envs differed significantly in their sensitivity to the CCR5 inhibitors maraviroc, CMPD-167 and SCH-412147. Inhibitor mapping experiments demonstrated that maraviroc, CMPD-167 and SCH-412147 interfered with the binding of CCR5 mAb to the C-terminal half of the second extracellular loop 2 of CCR5. Interestingly, Envs resistant to maraviroc, CMPD167 and SCH-412147 remained sensitive to TAK-779. Further studies indicated that the sensitivity of Envs to CCR5 inhibitors correlated with the molecular anatomy of CCR5 use, revealing that the inhibitor-sensitive Envs barely used the CCR5 N terminus, whereas resistant Envs showed a marked increase in its use. Taken together, these findings demonstrate that T/F R5 Envs are heterogeneous with respect to the mechanisms of CCR5 utilization. These data may have implications for therapeutic and prophylactic use of CCR5-based antiretrovirals.
TCP-Splitter: A TCP/IP flow monitor in reconfigurable hardware

TCP/IP is the most commonly-used protocol on the Internet. It provides a reliable transport for nearly all applications that utilize a network. These include Web browsers, FTP, Telnet, Secure Shell and other applications. New types of routers require the examination of TCP/IP flows transiting this networking equipment. This paper describes TCP-Splitter, a reconfigurable hardware based solution for analyzing and processing TCP/IP flows at multi-gigabit line rates. A consistent byte stream is delivered to a client application for every TCP/IP connection processed by TCP-Splitter. In order to maintain a design that is lightweight, efficient, and able to process a nearly unlimited number of flows at gigabit line rates, the system uses a non-passive flow processing algorithm.
Generalized Integrated Functional Test for Regional Methylation Rates

Motivation: Methods are needed to test pre-defined genomic regions such as promoters for differential methylation in genome-wide association studies, where the number of samples is limited and the data have large amounts of measurement error. Results: We developed a new statistical test, the generalized integrated functional test (GIFT), which tests for regional differences in methylation based on differences in the functional relationship between methylation percent and location of the CpG sites within a region. In this method, subject-specific functional profiles are first estimated, and the average profile within groups is compared between groups using an ANOVA-like test. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing functions can be used to estimate the functional relationship between methylation percent and CpG site location. Availability and Implementation: Matlab code for GIFT and sample data are available at this http URL Contact: rpodolsk@med.wayne. edu or dryu@gru.edu
Removal of Methylene Blue Using Chemically Modified Sugarcane Bagasse

Methylene Blue (MB) has been found to be one of the most common dyes used in the industries. Adsorption process using Activated Carbon (AC) has been proven to be able to remove MB effectively but the treatment cost using the adsorbent is considered expensive due to its high energy cost. Sugarcane Bagasse (SGB) is an agricultural by-product and abundantly available material in many developing countries. FTIR and XRD were used to confirm the existence of ligno-cellulose content of SGB after experiencing various chemical treatments. SGB had 5 - 40 folds higher MB removal capability than commercial activated carbon, depending on the pH of water medium and the type of SGB. SGB showed a much better performance in adsorbing MB in alkaline environment than in acidic environment. Langmuir adsorption isotherm model was able to estimate the removal capacity of non-chemical treated SGB (NSGB) and CaCl2 treated SGB (CSGB) at 84.7458 mg/g and 35.2113 mg/g respectively. An extremely higher MB removal capacity was found for BSGB due to the complexity of the surface site after chemical treatment. NaOH treated SGB (BSGB) with low lignin residue content was the most favourable adsorbent for MB adsorption.
Human Brain Regions Involved in Heading Estimation

Observer motion in a stationary visual environment results in an optic flow pattern on the retina, which in simple situations can be used to determine the direction of self motion or heading. The present study, using positron emission tomography (PET) and functional magnetic resonance imaging (fMRI), investigated the human cerebral activation pattern, elicited when subjects viewing a ground plane optic flow pattern actively judged heading. Several successive experiments controlled for visual input, visuospatial attention, and motor response effects. Results indicate that the network specifically involved in heading consists of only two motion sensitive areas: human MT/V5+, including an inferior satellite, and dorsal intraparietal sulcus area (DIPSM/L), predominantly in the right hemisphere, plus a dorsal premotor region bilaterally. These results suggest possible homologies with the dorsal part of the medial superior temporal area and area 7a in the monkey.
Defect Management Life Cycle Process for Software Quality Improvement

Software quality issues require special attention especially in view of the demands of quality software product to meet customer satisfaction. Software development projects in most organisations need proper defect management process in order to produce high quality software product and reduce the number of defects. The research question of this study is how to produce high quality software and reducing the number of defects. Therefore, the objective of this paper is to provide a framework for managing software defects by following defined life cycle processes. The methodology starts by reviewing defects, defect models, best practices and standards. A framework for defect management life cycle is proposed. The major contribution of this study is to define a defect management roadmap in software development. The adoption of an effective defect management process helps to achieve the ultimate goal of producing high quality software products and contributes towards continuous software process improvement.
Wood Filters as an Innovative Treatment Method for Roadway Runoff Pollutants

A significant amount of contamination enters water bodies via stormwater runoff. To control this non-point source pollution problem, retention ponds are installed at many locations. In previous studies it has been shown that these ponds do not effectively remove dissolved constituents, such as heavy metals and polycyclic aromatic hydrocarbons (PAHs). Results from previous laboratory tests suggest that wood fibers enhance the removal of dissolved contaminants from simulated runoff. Described in this report are the results of a pilot-scale wood filter test that was conducted at a retention pond in Providence, RI. One objective was to determine if wood fibers could effectively remove contaminants from the water under field conditions. A total of four filters were installed to determine sorption of nitrate, phosphate, copper, iron, zinc, and PAHs as a function of differences in wood mass, different residence times, and changes in temperature and pH. The wood filters effectively removed between 25% and 36% of the dissolved PAH contaminants. However, simple design changes promise to enhance the filter efficiency to about 50%. The heavier molecular weight PAH compounds, i.e., the PAHs with higher organic carbon partitioning coefficients (e.g., benzo(a)pyrene), sorbed more readily than the lighter molecular weight compounds. The PAH sorption effectiveness of Aspen wood was not affected by temperature or pH; however, the greater the mass of wood, the greater the sorption and effectiveness. The wood fibers appeared to promote nitrification, increasing the nitrate levels in the water, especially in the winter. The filters were 24% effective in removing phosphate from the water, but the wood leached phosphate after installation for a few days. Both copper (29%) and iron (40%) were effectively removed, especially under slightly acidic conditions. Zinc results were inconclusive because of zinc leaching from the galvanized wire mesh used to contain the wood fibers. Intense precipitation caused the filter to be less effective, and even flushed PAHs off the filter. The laboratory tests demonstrated that Cedar wood is a very promising alternative to Aspen wood. Even after more than 50 days of continuous flushing with contaminated water, the PAH removal remained between 66% and 92%, depending on the compound studied.
Molecular phylogenetic evidence supports a new family of octocorals and a new genus of Alcyoniidae (Octocorallia, Alcyonacea)

Abstract Molecular phylogenetic evidence indicates that the octocoral family Alcyoniidae is highly polyphyletic, with genera distributed across Octocorallia in more than 10 separate clades. Most alcyoniid taxa belong to the large and poorly resolved Holaxonia–Alcyoniina clade of octocorals, but members of at least four genera of Alcyoniidae fall outside of that group. As a first step towards revision of the family, we describe a new genus, Parasphaerasclera gen. n. , and family, Parasphaerascleridae fam. n. , of Alcyonacea to accommodate species of Eleutherobia Pütter, 1900 and Alcyonium Linnaeus, 1758 that have digitiform to digitate or lobate growth forms, completely lack sclerites in the polyps, and have radiates or spheroidal sclerites in the colony surface and interior. Parasphaerascleridae fam. n. constitutes a well-supported clade that is phylogenetically distinct from all other octocoral taxa. We also describe a new genus of Alcyoniidae, Sphaerasclera gen. n. , for a species of Eleutherobia with a unique capitate growth form. Sphaerasclera gen. n. is a member of the Anthomastus–Corallium clade of octocorals, but is morphologically and genetically distinct from Anthomastus Verrill, 1878 and Paraminabea Williams & Alderslade, 1999, two similar but dimorphic genera of Alcyoniidae that are its sister taxa. In addition, we have re-assigned two species of Eleutherobia that have clavate to capitate growth forms, polyp sclerites arranged to form a collaret and points, and spindles in the colony interior to Alcyonium, a move that is supported by both morphological and molecular phylogenetic evidence.
A Prospective Randomized Trial of Acute Normovolemic Hemodilution Compared to Standard Intraoperative Management in Patients Undergoing Major Hepatic Resection

Background:Hepatic resection is the most effective treatment for many malignant and benign conditions affecting the liver and biliary tree. Despite improvements, major partial hepatectomy can be associated with considerable blood loss and transfusion requirements. Transfusion of allogeneic blood products, although potentially life-saving, is associated with many potential complications. The primary aim of this study was to determine if acute normovolemic hemodilution (ANH), an established blood conservation technique, reduces the requirement for allogeneic red cell transfusions in patients undergoing major hepatic resection. Methods:One hundred thirty patients undergoing major hepatic resection (≥3 segments) were prospectively randomized to undergo either ANH or standard anesthetic management (STD). In the ANH group, intraoperative blood collection was performed to a target hemoglobin of 8.0 g/dL. Low central venous pressure anesthetic technique was used intraoperatively for both groups. A standardized transfusion protocol was applied to all patients intraoperatively and throughout the hospital stay. Results:From April 2004 to March 2007, 63 patients were randomized to ANH and 67 to STD. Demographics, diagnoses, liver function, extent of resection, intraoperative blood loss, operative time, incidence and grade of complications, and length of hospital stay were similar between the 2 groups. ANH reduced the overall allogeneic red cell transfusion rate by 50% compared with STD [12.7% (n = 8) vs. 25.4% (n = 17), respectively; P = 0.067. ANH patients were less often transfused intraoperatively (n = 1, 1.6%) compared with the STD group (n = 7, 10.4%) (P = 0.036), had higher postoperative hemoglobin levels (P = 0.01), and tended to require fewer red cell units overall (28 vs. 47 units). In patients with intraoperative blood loss ≥800 mL, ANH reduced not only the allogeneic red cell transfusion rate (18.2% vs. 42.4%, P = 0.045) but also the proportion of patients requiring fresh frozen plasma (21.1% vs. 48.3%, P = 0.025). Conclusion:For patients undergoing major liver resection, ANH is safe, effectively reduces the need for allogeneic transfusions, and should be considered for routine use. Given the modest transfusion rate in the STD arm, future efforts should attempt to target ANH use to patients most likely to benefit.
Classifying Cue Phrases in Text and Speech Using Machine Learning

Cue phrases may be used in a discourse sense to explicitly signal discourse structure, but also in a sentential sense to convey semantic rather than structural information. This paper explores the use of machine learning for classifying cue phrases as discourse or sentential. Two machine learning programs (CGRENDEL and C4.5) are used to induce classification rules from sets of pre-classified cue phrases and their features. Machine learning is shown to be an effective technique for not only automating the generation of classification rules, but also for improving upon previous results.