Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative genome analysis of commensal segmented �lamentous bacteria (SFB) from turkey and murine hosts reveals distinct metabolic features

Background: Segmented �lamentous bacteria (SFB) are intestinal commensal microorganisms that have been demonstrated to induce the innate and adaptive immune responses in mouse and rat hosts. SFB are Gram-positive, spore-forming bacteria that fail to grow in vitro due to unique metabolic requirements. Recently, SFB have been implicated in improved health and growth outcomes in commercial turkey �ocks. To assess the nature of SFB in turkeys and how they may differ from mammalian-associated SFB, the genome of turkey-associated SFB was compared with six representative genomes from murine hosts using an in silico approach. Results: The SFB-turkey genome is 1.6 Mb in length with a G+C content of 26.14%, and contains 1,604 coding sequences (CDS). Comparative genome analyses revealed that all the seven SFB strain possesses a shared set of metabolic de�ciencies and auxotrophies, speci�cally the inability of all the SFB strains to synthesize most of the amino acids, nucleotides and cofactors, emphasizing the importance of metabolite acquisition from the host intestinal environment. Among the seven SFB genomes, the SFB-turkey genome is the largest and contains the highest number of predicted CDS. The SFB-turkey genome possesses cellular metabolism genes that are absent in the rodent SFB strains including catabolic pathways for sucrose, stachyose, ra�nose and other complex glycans. Other unique genes associated with SFB-turkey genome is loci for the biosynthesis of biotin, and degradation enzymes to recycle primary bile acids, both of which may play an important role to help turkey associated SFB survive and secure mutualism with its avian host. Conclusions: Comparative genomic analysis of seven SFB genomes revealed that each of the strains have a core set of metabolic capabilities and de�ciencies that make these bacteria challenging to culture ex vivo. When compared to the murine-associated strains, turkey-associated SFB serves as a phylogenetic outgroup and a unique member among all the sequenced strains of SFB. This turkey-associated SFB strain is the �rst reported non-mammalian SFB genome, and highlights the impact of host speci�city on the evolution of metabolic capabilities. substrates, break down complex glycans, hydrolyze and recycle primary bile acids, and synthesize, rather than degrade biotin. Differences in these strains may provide further insights into the impact of coevolution with a given host organism on the development of novel characteristics.
Using Social Media Content to Inform Agent-based Models for Humanitarian Crisis Response

Crisis response is a time-sensitive problem with multiple concurrent and interacting subprocesses, applied around the world in a wide range of contexts and with access to varying levels of resources. The movement of individuals with their shifting patterns of need and, frequently, disrupted normal support systems pose challenges to responders trying to understand what is needed, where, and when. Unfortunately, crises frequently occur in parts of the world that lack the infrastructure to respond to them and the information to inform responders where to target their efforts. In light of these challenges, researchers can make use of new data sources and technologies, combining the information products with simulation techniques to gain knowledge of the situation and to explore the various ways in which a crisis may develop. These new data sources - including social media such as Twitter and volunteered geographic information (VGI) from groups such as OpenStreetMap - can be combined with authoritative data sources in order to create rich, synthetic datasets, which may in turn be subjected to processes such as sentiment analysis and social network analysis. Further, these datasets can be transformed into information which supports powerful agent- based models (ABM). Such models can capture the behavior of heterogeneous individuals and their decision-making process, allowing researchers to explore the emergent dynamics of crisis situations. To that end, this research explores the gathering, cleaning, and synthesis of diverse data sources as well as the information which can be extracted from such synthetic data sources. Further, the work presents a rich, behaviorally complex agent-based model of an evacuation effort. The case study deals with the 2012 Colorado Wildfires, which threatened the city of Colorado Springs and prompted the evacuation of over 28,000 persons over the course of four days. The model itself explores how a synthetic population with automatically generated synthetic social networks communicates about and responds to the developing crisis, utilizing real evacuation order information as well as a model of wildfire development to which the individual agents respond. This research contributes to the study of data synthesis, agent-based modeling, and crisis development.
“I'm walking on eggshells”: Challenges faced by mothers with breast cancer in interacting with adolescent daughters

Background With breast cancer becoming the most diagnosed cancer in the world, the number of breast cancer mothers with adolescent children is also rising. And for adolescent daughters, their mother server as a primary figure among the key processes of identification with their gender, femininity and sexuality. But breast cancer threats mother’s health including such a key symbol of her womanhood, the breast. Which may adversely affect the development of an adolescent daughter’s own sense of personal identity and womanhood. However, few researchers and practitioners on mother-daughter interactions in the context of breast cancer, therefor this study is aimed to reveal the nuances of interactive challenges with adolescent daughters faced by mother with breast cancer from mother’ perspective. Methods A qualitative study was conducted. With the sample saturation principle, data collected by semi-structured interviews with 21 breast cancer patients who are in line with breast conserving. Colaizzi’s method of phenomenology was used for data analysis and Foucauldian discourse approach was also partially integrated into the analysis for this research. Results Three major themes emerged from the data. The themes were the following: (1) Mothers are lost in chaos (unable to deal with the shock of cancer, powerlessness of the uncertainty about the life span, and confused about how to respond to daughter's curiosity); (2) Mothers struggle for balance (protect daughter or let her be independent, as a mother or a patient); and (3) Mothers are immersed in guilt (increasing risk of cancer for daughters, influencing the development of daughter, and bring burden to daughter). Conclusions Our findings explore the interaction experience of breast cancer mothers and adolescence daughters, and further reveal the nuances of mother–daughter interaction challenges faced by mother with breast cancer from mother’ perspective. To help mothers enhance interaction with their daughters and assist health practitioners to translate our findings into health interventions.
An examination of hazard communication logs and public response during the 1946 and 1960 tsunamis that impacted Hilo, Hawaii

Abstract This paper examines communication methods used to inform the vulnerable community of Hilo, Hawaii of the impending tsunamis that struck in 1946 and 1960. These tsunamis caused tragic loss of life and enormous economic damage in Hilo and along the shores of the Hawaiian Island chain. Over 12 h notice of a possible large tsunami was given in 1960 and the siren warning system sounded more than 4 h prior to the event. The government agencies knew there was a tsunami alert and the media were broadcasting warnings. However, the 1960 tsunami took the lives of 61 people in Hilo only 14 years after 96 people were killed during the 1946 event. In order to discover why so many people perished, government agency logs recorded during the 1960 tsunami were examined and personal accounts from survivors of both the 1946 and 1960 tsunamis were analysed. Contributing to the tragic loss of life was a lack of communication between government agencies in addition to media inaccuracies and a public that was not educated in tsunami safety. Effective tsunami mitigation can only be accomplished through continual tsunami awareness education for the public, media and emergency personnel, and with accurate and timely tsunami warnings.
Transnational civil society and the consumer-friendly turn in financial regulation

The literature on financial regulation has typically emphasized the role of the powerful financial industry in shaping regulatory outcomes. However, capture theories cannot explain the prominence of financial consumer protection in post-crisis reform agendas. By contrast, this paper argues that, despite their collective action disadvantage, a polymorphous network of civil society organizations was able to gain momentum after the financial crisis and to influence the financial reform process. In this policy window, where decision-makers were looking out for an alternative source of expertise, a transnationally connected civil society network successfully raised the issue of consumer protection on reform agendas in tandem with public entrepreneurs and on the back of a popular backlash against big finance. This argument will be explored through a comparative study of the impact of transnational pressures on policy-makers in Europe and the US in the immediate aftermath of the crisis. In the conclusion, the paper discusses the substance of the financial reforms that have been undertaken.
Acute Exercise Increases Nitric Oxide Synthase Activity in Skeletal Muscle

Acute exercise increases nitric oxide synthase activity in skeletal muscle. Am. —This study examined the effects of acute exercise on skeletal muscle nitric oxide synthase (NOS) activity. Female Sprague-Dawley rats were divided into three groups: control, exercise, and exercise ϩ N G-nitro-L-arginine methyl ester (L-NAME). In the exercise ϩ L-NAME group, L-NAME was administered in the drinking water (1 mg/ml) for 2 days and subsequently the exercise and exercise ϩ L-NAME groups underwent a 45-min bout of exhaustive treadmill running after which NOS activity and muscle glycogen were measured. In the control and exercise groups, 1-amino-S-methylisothiourea (AMITU), a selective neuronal NOS inhibitor, with and without additional nonse-lective NOS blockade [with N G-monomethyl-L-arginine (L-NMMA)], was used in vitro to assess the contribution of nNOS to total NOS activity. The exercise bout increased NOS activity by 37% in exercise compared with control groups, and both groups had significantly greater NOS activity compared with exercise ϩ L-NAME. AMITU decreased total NOS activity in the control and exercise groups by 31.8 and 30.2%, respectively, and these activities were significantly greater than AMITU ϩ L-NMMA in both control and exercise groups. We conclude that 1) there is basal neuronal NOS and endothelial NOS activity in skeletal muscle, 2) an acute exercise bout increases NOS activity in skeletal muscle, and 3) glycogen depletion during exercise occurs irrespective of NOS activity. 1-amino-S-methylisothiourea; glycogen; muscle contraction NITRIC OXIDE (NO) is a signaling molecule formed from L-arginine by a number of different isoforms of nitric oxide synthase (NOS; Ref. 19). Both the neuronal NOS (nNOS) and the endothelial NOS (eNOS) isoforms are expressed in skeletal muscle (12, 13). nNOS is thought to be localized in the subsarcolemmal region of skeletal muscle and at the neuromuscular junction (12, 14), whereas eNOS is uniformly distributed in muscle fibers (13) as well as being located in the vessel wall. In addition, it has been demonstrated that both fast-and slow-twitch skeletal muscle can express both nNOS and eNOS protein (12, 13, 26). The quantity of the nNOS isoform appears to be related to the fiber-type distribution of a particular muscle, i.e., higher nNOS levels are associated with fast-twitch-glycolytic muscles (12). On the other hand, eNOS levels are associated with more oxidative muscles (13). Balon and Nadler (3) were the first to demonstrate an increase in NO release from muscles exposed to prior electrical stimulation. Prior exercise increases NO me-tabolite production (11), and NO concentrations …
Aquia Aquifer Dissolved Cl− and 36Cl/Cl: Implications for Flow Velocities

The Aquia aquifer (southern Maryland) contains a remarkably smooth Cl− profile (0.46–3.23 ppm) along its flow path. This is interpreted as a record of historic changes in the deposition of Cl− in this region. Those changes have been influenced by the rise and fall of sea level, which has altered the distance of the recharge region from the coastline by ∼200 km. The 36Cl concentration along the flow path is not as smooth as the Cl− profile. Historic variations in cosmogenic production, atmospheric transport, precipitation, and evapotranspiration all might have influenced 36Cl concentrations. A general similarity between the 36Cl and Cl− profiles suggests that changes in precipitation and evapotranspiration rates, which influence both tracers similarly, are particularly important. To reconcile 14C, 36Cl, and hydrologic data, we propose a two-tier model for flow in the Aquia. Shallower portions of the aquifer (<60 m) were subjected to hydraulic gradients and flow rates approximately 5 times larger during the Pleistocene than modern, prepumping rates. At greater depths, flow rates were much slower and less variable; water in this region may be old enough to record some 36Cl decay.
Cyclin-dependent kinase inhibitors: a survey of the recent patent literature

Since the mid-1990s cyclin-dependent kinase (CDK) inhibition has been the subject of an intense drug discovery effort in the pharmaceutical industry and in some academic institutions. Although only few compounds have at present progressed into human clinical trials, the prospect of finding safe agents useful in therapy, particularly in the cancer setting, is still positive. Some trends can be observed that witness the impact of recent findings in CDK basic biological research and technology advancements on the evolution of the patent literature on CDK inhibition. A patent literature review of small organic molecules as CDK inhibitors comprising the years 2001 – 2004 is presented here, as many of the major pharmaceutical companies have shown a continued effort in the field.
Suspension of bed material over sand bars in the Lower Mississippi River and its implications for Mississippi delta environmental restoration

Understanding specific pathways for sand transport in the lower reaches of large rivers, including the Mississippi, is a key for addressing multiple significant geologic problems, such as delta building and discharge to the oceans, and for environmental restoration efforts in deltaic environments threatened by rising sea levels. Field studies were performed in the Mississippi River 75–100 km upstream of the Gulf of Mexico outlet in 2010–2011 to examine sand transport phenomena in the tidally affected river channel over a range of discharges. Methods included mapping bottom morphology (multibeam sonar), cross‐sectional and longitudinal measurements of water column velocity and acoustic backscatter, suspended sediment sampling, and channel‐bed sampling. Substantial interaction was observed between the flow conditions in the river (boundary shear stress), channel‐bed morphology (size and extent of sandy bedforms), and bed material sand transport (quantity, transport mode, and spatial distribution). A lateral shift was observed in the region of maximum bed material transport from deep to shallow areas of subaqueous sand bars with increasing water discharge. Bed material was transported both in traction and in suspension at these water discharges, and we posit that the downriver flux of sand grains is composed of both locally‐ and drainage basin‐sourced material, with distinct transport pathways and relations to flow conditions. We provide suggestions for the optimal design and operation of planned river diversion projects.
Temporal variability and tidal modulation of hydrothermal exit‐fluid temperatures at the Lucky Strike deep‐sea vent field, Mid‐Atlantic Ridge

We deployed autonomous temperature sensors at black smoker chimneys, cracks, and diffuse flow areas at the Lucky Strike hydrothermal field (Mid‐Atlantic Ridge, ~37°17'N) between summer 2009 and summer 2012 and contemporaneously measured tidal pressures and currents as part of the long‐term MoMAR experiment to monitor hydrothermal activity. We classify the temperature data according to the hydrogeologic setting of the measurement sites: a high‐temperature regime (>190°C) representing discharge of essentially unmixed, primary hydrothermal fluids through chimneys, an intermediate‐temperature regime (10–100°C) associated with mixing of primary fluids with cold pore fluids discharging through cracks, and a low‐temperature regime (<10°C) associated with a thermal boundary layer forming over bacterial mats associated with diffuse outflow of warm fluids. Temperature records from all the regimes exhibit variations at semi‐diurnal tidal periods, and cross‐spectral analyses reveal that high‐temperature discharge correlates to tidal pressure while low‐temperature discharge correlates to tidal currents. Intermediate‐temperature discharge exhibits a transitional behavior correlating to both tidal pressure and currents. Episodic perturbations, with transient temperature drops of up to ~150°C, which occur in the high‐temperature and intermediate‐temperature records, are not observed on multiple probes (including nearby probes at the same site), and they are not correlated with microearthquake activity, indicating that the perturbation mechanism is highly localized at the measurement sites within the hydrothermal structures. The average temperature at a given site may increase or decrease at annual time scales, but the average temperature of the hydrothermal field, as a whole, appears to be stable over our 3 year observation period.
Can Distributed Volunteers Accomplish Massive Data Analysis Tasks

The science community is accustomed to interacting with the public for two main purposes: outreach to adults (since they are the patrons upon whose good will future funding will depend), and education for children (since they are the reservoir from which the next generation's talent must be drawn). We suggest that a third relationship can now be fruitful, one that has been little used until now - with the notable exception of the astronomy community. Astronomy has a long history of relying on non-professionals for some observations. Important contributions have been made by amateur astronomers in several areas of research including monitoring dust storms on Mars, timing asteroid occultations, and discovering comets. Note that three distinct contributions are being made by amateur astronomers: they supply their own instrumentation, provide access to observing sites around the Globe, and contribute their innate powers of perception.
Eocene sedimentation and tectonics in the Hampshire Basin

Sedimentary evidence in the Eocene (Cuisian-Lutetian) of the Hampshire Basin indicates important intra-Eocene movement on the Isle of Wight and Purbeck Monoclines, and on the Ridgeway Fault. Evidence for syn-depositional movement includes Jurassic and Cretaceous chert and flint pebbles in the Eocene, the distribution of which suggests derivation from both E and W. At Whitecliff Bay, two units of cross-bedded sand have northward-directed palaeocurrents and may have been deposited as localized fans of debris reworked from earlier Tertiary sediments on the upwarped side of the monocline. Three units of laminated muds are intercalated with marine sediments in the eastern part of the basin and suggest periods of low salinity, tideless conditions. These episodes are attributed to the periodic isolation of the Hampshire Basin from the fully marine Dieppe Basin to the SE. This may have been the result of intermittent movement on a tectonic barrier to the SE of Selsey. The onset of uplift and subsequent exposure of the Chalk along the southern margin of the basin proceeded unevenly from ? early Cuisian to late Lutetian times. Movement on the Portsdown Anticline probably occurred over a similar period. The Isle of Wight and Purbeck Monoclines are the superficial expressions of faults in the Palaeozoic basement, and not the result of lateral ‘Alpine’ pressures. A minor series of syn-depositional folds trend NW-SE across the basin and may reflect a component of sinistral strike-slip on basement faults.
The evolution of altruistic social preferences in human groups

In this paper, we consider three hypotheses to account for the evolution of the extraordinary capacity for large-scale cooperation and altruistic social preferences within human societies. One hypothesis is that human cooperation is built on the same evolutionary foundations as cooperation in other animal societies, and that fundamental elements of the social preferences that shape our species' cooperative behaviour are also shared with other closely related primates. Another hypothesis is that selective pressures favouring cooperative breeding have shaped the capacity for cooperation and the development of social preferences, and produced a common set of behavioural dispositions and social preferences in cooperatively breeding primates and humans. The third hypothesis is that humans have evolved derived capacities for collaboration, group-level cooperation and altruistic social preferences that are linked to our capacity for culture. We draw on naturalistic data to assess differences in the form, scope and scale of cooperation between humans and other primates, experimental data to evaluate the nature of social preferences across primate species, and comparative analyses to evaluate the evolutionary origins of cooperative breeding and related forms of behaviour.
Comportamiento aerobiológico del polen de algunos taxones herbáceos riparios en Salamanca (centro-oeste de la Península Ibérica)

Atmospheric pollen levels of Cyperaceae, Juncaceae and Typhaceae were studied in 2000-2007 period by means of a Hirst Volumetric Spore Trap in the city of Salamanca (MW Spain). The intra-diurnal pattern and the influence of selected meteorological parameters in Cyperaceae airborne pollen concentrations were also analysed. Seasonal distribution was focused between May and August for Cyperaceae and Juncaceae, between late May and mid-October for Typhaceae. In addition, their airborne pollen levels did not overcome 10 grains/m3. In the case of Cyperaceae, intra-diurnal distribution showed greater levels between 11 and 20 hours, and temperature, insolation and NE-N winds had a positive influence in atmospheric concentrations, whereas rainfall and relative humidity displayed negative correlation coefficients with Cyperaceae pollen concentrations.