Miracle-dz/UniFAR-FTUs huggingface dataset:
Fish Biodiversity of the Vitória-Trindade Seamount Chain, Southwestern Atlantic: An Updated Database

Despite a strong increase in research on seamounts and oceanic islands ecology and biogeography, many basic aspects of their biodiversity are still unknown. In the southwestern Atlantic, the Vitória-Trindade Seamount Chain (VTC) extends ca. 1,200 km offshore the Brazilian continental shelf, from the Vitória seamount to the oceanic islands of Trindade and Martin Vaz. For a long time, most of the biological information available regarded its islands. Our study presents and analyzes an extensive database on the VTC fish biodiversity, built on data compiled from literature and recent scientific expeditions that assessed both shallow to mesophotic environments. A total of 273 species were recorded, 211 of which occur on seamounts and 173 at the islands. New records for seamounts or islands include 191 reef fish species and 64 depth range extensions. The structure of fish assemblages was similar between islands and seamounts, not differing in species geographic distribution, trophic composition, or spawning strategies. Main differences were related to endemism, higher at the islands, and to the number of endangered species, higher at the seamounts. Since unregulated fishing activities are common in the region, and mining activities are expected to drastically increase in the near future (carbonates on seamount summits and metals on slopes), this unique biodiversity needs urgent attention and management.
Do Social Networks Influence Small-Scale Fishermen’s Enforcement of Sea Tenure?

Resource systems with enforced rules and strong monitoring systems typically have more predictable resource abundance, which can confer economic and social benefits to local communities. Co-management regimes demonstrate better social and ecological outcomes, but require an active role by community members in management activities, such as monitoring and enforcement. Previous work has emphasized understanding what makes fishermen comply with rules. This research takes a different approach to understand what influences an individual to enforce rules, particularly sea tenure. We conducted interviews and used multiple regression and Akaike’s Information Criteria model selection to evaluate the effect of social networks, food security, recent catch success, fisherman’s age and personal gear investment on individual’s enforcement of sea tenure. We found that fishermen’s enforcement of sea tenure declined between the two time periods measured and that social networks, age, food security, and changes in gear investment explained enforcement behavior across three different communities on Nicaragua’s Atlantic Coast, an area undergoing rapid globalization.
Chemical Composition and Biological Activities of Trans-Himalayan Alga Spirogyra porticalis (Muell.) Cleve

The freshwater alga Spirogyra porticalis (Muell.) Cleve, a filamentous charophyte, collected from the Indian trans-Himalayan cold desert, was identified on the basis of morpho-anatomical characters. Extracts of this alga were made using solvents of varying polarity viz. n-hexane, acetonitrile, methanol and water. The antioxidant capacities and phenolic profile of the extracts were estimated. The methanol extract showing highest antioxidant capacity and rich phenolic attributes was further investigated and phytochemical profiling was conducted by gas chromatography-mass spectrometry (GC/MS) hyphenated technique. The cytotoxic activity of methanol extract was evaluated on human hepatocellular carcinoma HepG2 and colon carcinoma RKO cell lines. The anti-hypoxic effect of methanol extract of the alga was tested on in vivo animal system to confirm its potential to ameliorate oxidative stress. The antioxidant assays viz. ferric reducing antioxidant power (FRAP), 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS), 1,1-diphenyl-2-picrylhydrazyl (DPPH) and nitric oxide (NO) radical scavenging capacities, β-carotene-linoleic acid bleaching property and lipid peroxidation exhibited analogous results, wherein the algal extracts showed significantly high antioxidant potential. The extracts were also found to possess high content of total proanthocyanidin, flavonoid and polyphenol. GC/MS analysis revealed the presence of thirteen chemotypes in the methanol extract representing different phytochemical groups like fatty acid esters, sterols, unsaturated alcohols, alkynes etc. with substantial phyto-pharmaceutical importance. The methanol extract was observed to possess anticancer activity as revealed from studies on HepG2 and RKO cell lines. In the present study, S. porticalis methanol extract also provided protection from hypoxia-induced oxidative stress and accelerated the onset of adaptative changes in rats during exposure to hypobaric hypoxia. The bioactive phytochemicals present in this trans-Himalayan alga are of enormous interest and can be utilized sustainably for discovery of novel drugs against oxidative stress.
Estimating Annual Soil Carbon Loss in Agricultural Peatland Soils Using a Nitrogen Budget Approach

Around the world, peatland degradation and soil subsidence is occurring where these soils have been converted to agriculture. Since initial drainage in the mid-1800s, continuous farming of such soils in the California Sacramento-San Joaquin Delta (the Delta) has led to subsidence of up to 8 meters in places, primarily due to soil organic matter (SOM) oxidation and physical compaction. Rice (Oryza sativa) production has been proposed as an alternative cropping system to limit SOM oxidation. Preliminary research on these soils revealed high N uptake by rice in N fertilizer omission plots, which we hypothesized was the result of SOM oxidation releasing N. Testing this hypothesis, we developed a novel N budgeting approach to assess annual soil C and N loss based on plant N uptake and fallow season N mineralization. Through field experiments examining N dynamics during growing season and winter fallow periods, a complete annual N budget was developed. Soil C loss was calculated from SOM-N mineralization using the soil C:N ratio. Surface water and crop residue were negligible in the total N uptake budget (3 – 4 % combined). Shallow groundwater contributed 24 – 33 %, likely representing subsurface SOM-N mineralization. Assuming 6 and 25 kg N ha-1 from atmospheric deposition and biological N2 fixation, respectively, our results suggest 77 – 81 % of plant N uptake (129 – 149 kg N ha-1) was supplied by SOM mineralization. Considering a range of N uptake efficiency from 50 – 70 %, estimated net C loss ranged from 1149 – 2473 kg C ha-1. These findings suggest that rice systems, as currently managed, reduce the rate of C loss from organic delta soils relative to other agricultural practices.
Prevalence and Perinatal Outcomes of Singleton Term Breech Delivery in Wolisso Hospital, Oromia Region, Southern Ethiopia: A Cross-Sectional Study

Background Breech deliveries have always been topical issues in obstetrics. Neonates undergoing term breech deliveries have long-term morbidity up to the school age irrespective of mode of delivery. Objective To determine prevalence and perinatal outcomes of singleton term breech delivery. Methods Hospital based cross-sectional study was conducted on 384 participants retrospectively. Descriptive and analytical statistics was used. Result A total of 384 breech deliveries were included. Prevalence of singleton breech deliveries in the hospital was 3.4%. The perinatal outcome of breech deliveries was 322 (83.9%). Adverse perinatal outcome of singleton term breech delivery was significantly associated with women's age of greater than or equal to 35 years (AOR = 2.62, 95% CI = 1.14–6.03), fully dilated cervix (AOR = 0.48, 95% CI = 0.25–0.91), ruptured membrane (AOR = 5.11, 95% CI = 2.25–11.6), and fetal weight of <2500 g (AOR = 6.77, 95% CI = 3.22–14.25). Conclusion Entrapment of head, birth asphyxia, and cord prolapse were the most common causes of perinatal mortality. Factors like fetal weight <2500 gm, mothers of age 35 years and above, those mothers not having a fully dilated cervix, and mothers with ruptured membrane were associated with increased perinatal mortality.
Electronic structure of URu2Si2 studied by photoelectron spectroscopy (INVITED)

aCondensed Matter Science Division, Japan Atomic Energy Agency, Sayo, Hyogo, 679-5148, Japan; Department of Physics, University of Tokyo, Hongo, Tokyo, 113-0033, Japan; Department of Physics, Faculty of Science, Kyoto Sangyo University, Kyoto, 603-8555, Japan; Advanced Science Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, 319-1195, Japan; Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
Proliferation and Differentiation Potential of Human Adipose-Derived Stem Cells Grown on Chitosan Hydrogel

Applied tissue engineering in regenerative medicine warrants our enhanced understanding of the biomaterials and its function. The aim of this study was to evaluate the proliferation and differentiation potential of human adipose-derived stem cells (hADSCs) grown on chitosan hydrogel. The stability of this hydrogel is pH-dependent and its swelling property is pivotal in providing a favorable matrix for cell growth. The study utilized an economical method of cross linking the chitosan with 0.5% glutaraldehyde. Following the isolation of hADSCs from omentum tissue, these cells were cultured and characterized on chitosan hydrogel. Subsequent assays that were performed included JC-1 staining for the mitochondrial integrity as a surrogate marker for viability, cell proliferation and growth kinetics by MTT assay, lineage specific differentiation under two-dimensional culture conditions. Confocal imaging, scanning electron microscopy (SEM), and flow cytometry were used to evaluate these assays. The study revealed that chitosan hydrogel promotes cell proliferation coupled with > 90% cell viability. Cytotoxicity assays demonstrated safety profile. Furthermore, glutaraldehyde cross linked chitosan showed < 5% cytotoxicity, thus serving as a scaffold and facilitating the expansion and differentiation of hADSCs across endoderm, ectoderm and mesoderm lineages. Additional functionalities can be added to this hydrogel, particularly those that regulate stem cell fate.
Cooperative Sequential Spectrum Sensing Based on Level-Triggered Sampling

We propose a new framework for cooperative spectrum sensing in cognitive radio networks, that is based on a novel class of nonuniform samplers, called the event-triggered samplers, and sequential detection. In the proposed scheme, each secondary user (SU) computes its local sensing decision statistic based on its own channel output; and whenever such decision statistic crosses certain predefined threshold values, the secondary user will send one (or several) bit of information to the fusion center (FC). The FC asynchronously receives the bits from different SUs and updates the global sensing decision statistic to perform a sequential probability ratio test (SPRT), to reach a sensing decision. We provide an asymptotic analysis for the above scheme, and under different conditions, we compare it against the cooperative sensing scheme that is based on traditional uniform sampling and sequential detection. Simulation results show that the proposed scheme, using even 1 bit, can outperform its uniform sampling counterpart that uses infinite number of bits under changing target error probabilities, SNR values, and number of SUs.
A Novel Mathematical Model Describing Adaptive Cellular Drug Metabolism and Toxicity in the Chemoimmune System

Cells cope with the threat of xenobiotic stress by activating a complex molecular network that recognizes and eliminates chemically diverse toxic compounds. This “chemoimmune system” consists of cellular Phase I and Phase II metabolic enzymes, Phase 0 and Phase III ATP Binding Cassette (ABC) membrane transporters, and nuclear receptors regulating these components. In order to provide a systems biology characterization of the chemoimmune network, we designed a reaction kinetic model based on differential equations describing Phase 0–III participants and regulatory elements, and characterized cellular fitness to evaluate toxicity. In spite of the simplifications, the model recapitulates changes associated with acquired drug resistance and allows toxicity predictions under variable protein expression and xenobiotic exposure conditions. Our simulations suggest that multidrug ABC transporters at Phase 0 significantly facilitate the defense function of successive network members by lowering intracellular drug concentrations. The model was extended with a novel toxicity framework which opened the possibility of performing in silico cytotoxicity assays. The alterations of the in silico cytotoxicity curves show good agreement with in vitro cell killing experiments. The behavior of the simplified kinetic model suggests that it can serve as a basis for more complex models to efficiently predict xenobiotic and drug metabolism for human medical applications.
In vivo engineering of bone tissues with hematopoietic functions and mixed chimerism

Significance Current bone marrow (BM) or hematopoietic stem cell (HSC) transplantations require recipient conditioning that is accompanied by significant adverse effects in patients. Here, we report engineering of bone tissues with a functional BM compartment in vivo by modular assembly of mineralized and nonmineralized macroporous structures. These engineered bone tissues support maintenance of donor hematopoietic cells, respond to an HSC mobilization agent, and yield higher mixed chimerism in circulation of nonirradiated recipient mice compared with that of intravenous transplantation. Such engineered bone tissues could potentially be used as ectopic BM surrogates to treat various nonmalignant BM diseases and as a tool to study hematopoiesis, donor–host cell dynamics, tumor tropism, and hematopoietic cell transplantation. Synthetic biomimetic matrices with osteoconductivity and osteoinductivity have been developed to regenerate bone tissues. However, whether such systems harbor donor marrow in vivo and support mixed chimerism remains unknown. We devised a strategy to engineer bone tissues with a functional bone marrow (BM) compartment in vivo by using a synthetic biomaterial with spatially differing cues. Specifically, we have developed a synthetic matrix recapitulating the dual-compartment structures by modular assembly of mineralized and nonmineralized macroporous structures. Our results show that these matrices incorporated with BM cells or BM flush transplanted into recipient mice matured into functional bone displaying the cardinal features of both skeletal and hematopoietic compartments similar to native bone tissue. The hematopoietic function of bone tissues was demonstrated by its support for a higher percentage of mixed chimerism compared with i.v. injection and donor hematopoietic cell mobilization in the circulation of nonirradiated recipients. Furthermore, hematopoietic cells sorted from the engineered bone tissues reconstituted the hematopoietic system when transplanted into lethally irradiated secondary recipients. Such engineered bone tissues could potentially be used as ectopic BM surrogates for treatment of nonmalignant BM diseases and as a tool to study hematopoiesis, donor–host cell dynamics, tumor tropism, and hematopoietic cell transplantation.
Optimal linear space-time spreading for multiuser MIMO communications

In this paper, we study the design of linear dispersion (LD) codes for uplink multiuser channels with multiple antennas at the base station and each mobile unit. In the considered scheme, each user employs LD codes to transmit the data, i.e., the transmitted codeword is a linear combination over space and time of certain dispersion matrices with the transmitted symbols. The linear space-time spreading can also be utilized to separate multiple users at the base station. We propose a simulation-based optimization method together with gradient estimation to systematically design the multiuser linear space-time coding under either optimal or suboptimal receivers. We perform the gradient estimation through the score function method. The proposed method can also be applied to design codes under different fading statistics. Simulation results show that under the optimal maximum-likelihood (ML) receiver, the codes obtained by the new algorithm provides roughly the same performance as the low-dimensional spread modulation, as well as the interference-resistant modulation. Moreover, the new codes perform significantly better with suboptimal multiuser receiver structures.
Physical activity across the lifespan and liver cancer incidence in the NIH‐AARP Diet and Health Study cohort

While liver cancer rates in the United States are increasing, 5‐year survival is only 17.6%, underscoring the importance of prevention. Physical activity has been associated with lower risk of developing liver cancer, but most studies assess physical activity only at a single point in time, often in midlife. We utilized physical activity data from 296,661 men and women in the NIH‐AARP Diet and Health Study cohort to test whether physical activity patterns over the life course could elucidate the importance of timing of physical activity on liver cancer risk. We used group modeling of longitudinal data to create physical activity trajectories using four time points across the life course from teenage years through middle age, identifying seven distinct trajectories. We then used Cox proportional hazards regression to assess the association between the physical activity trajectories and risk of hepatocellular carcinoma, the most common type of liver cancer. We found that, in adjusted analyses, compared to those with consistently low physical activity patterns, those who maintained activity levels over time had a 26–36% lower risk of liver cancer and those who increased physical activity over time had no associations with risk, while those who decreased activity over time had a nonsignificantly higher risk of liver cancer. Our results suggest that sustained physical activity is associated with lower risk of hepatocellular carcinoma, while increasing physical activity later in life may not yield the same benefit. Future research with larger sample sizes and more detailed data on dose and timing of physical activity may continue to yield insight into this association between physical activity and liver cancer risk.
Review of Recent Methodological Developments in Group-Randomized Trials: Part 2-Analysis

In 2004, Murray et al. reviewed methodological developments in the design and analysis of group-randomized trials (GRTs). We have updated that review with developments in analysis of the past 13 years, with a companion article to focus on developments in design. We discuss developments in the topics of the earlier review (e.g., methods for parallel-arm GRTs, individually randomized group-treatment trials, and missing data) and in new topics, including methods to account for multiple-level clustering and alternative estimation methods (e.g., augmented generalized estimating equations, targeted maximum likelihood, and quadratic inference functions). In addition, we describe developments in analysis of alternative group designs (including stepped-wedge GRTs, network-randomized trials, and pseudocluster randomized trials), which require clustering to be accounted for in their design and analysis.
Architecture and design of AlphaServer GS320

This paper describes the architecture and implementation of the AlphaServer GS320, a cache-coherent non-uniform memory access multiprocessor developed at Compaq. The AlphaServer GS320 architecture is specifically targeted at medium-scale multiprocessing with 32 to 64 processors. Each node in the design consists of four Alpha 21264 processors, up to 32GB of coherent memory, and an aggressive IO subsystem. The current implementation supports up to 8 such nodes for a total of 32 processors. While snoopy-based designs have been stretched to medium-scale multiprocessors by some vendors, providing sufficient snoop bandwidth remains a major challenge especially in systems with aggressive processors. At the same time, directory protocols targeted at larger scale designs lead to a number of inherent inefficiencies relative to snoopy designs. A key goal of the AlphaServer GS320 architecture has been to achieve the best-of-both-worlds, partly by exploiting the bounded scale of the target systems.This paper focuses on the unique design features used in the AlphaServer GS320 to efficiently implement coherence and consistency. The guiding principle for our directory-based protocol is to address correctness issues related to rare protocol races without burdening the common transaction flows. Our protocol exhibits lower occupancy and lower message counts compared to previous designs, and provides more efficient handling of 3-hop transactions. Furthermore, our design naturally lends itself to elegant solutions for deadlock, livelock, starvation, and fairness. The AlphaServer GS320 architecture also incorporates a couple of innovative techniques that extend previous approaches for efficiently implementing memory consistency models. These techniques allow us to generate commit events (which are used for ordering purposes) well in advance of formulating the reply to a transaction. Furthermore, the separation of the commit event allows time-critical replies to by-pass inbound requests without violating ordering properties. Even though our design specifically targets medium-scale servers, many of the same techniques can be applied to larger-scale directory-based and smaller-scale snoopy-based designs. Finally, we evaluate the performance impact of some of the above optimizations and present a few competitive benchmark results.
Importance of Tissue Preparation Methods in FTIR Micro-Spectroscopical Analysis of Biological Tissues: ‘Traps for New Users’

Fourier Transform Infrared (FTIR) micro-spectroscopy is an emerging technique for the biochemical analysis of tissues and cellular materials. It provides objective information on the holistic biochemistry of a cell or tissue sample and has been applied in many areas of medical research. However, it has become apparent that how the tissue is handled prior to FTIR micro-spectroscopic imaging requires special consideration, particularly with regards to methods for preservation of the samples. We have performed FTIR micro-spectroscopy on rodent heart and liver tissue sections (two spectroscopically very different biological tissues) that were prepared by desiccation drying, ethanol substitution and formalin fixation and have compared the resulting spectra with that of fully hydrated freshly excised tissues. We have systematically examined the spectra for any biochemical changes to the native state of the tissue caused by the three methods of preparation and have detected changes in infrared (IR) absorption band intensities and peak positions. In particular, the position and profile of the amide I, key in assigning protein secondary structure, changes depending on preparation method and the lipid absorptions lose intensity drastically when these tissues are hydrated with ethanol. Indeed, we demonstrate that preserving samples through desiccation drying, ethanol substitution or formalin fixation significantly alters the biochemical information detected using spectroscopic methods when compared to spectra of fresh hydrated tissue. It is therefore imperative to consider tissue preparative effects when preparing, measuring, and analyzing samples using FTIR spectroscopy.