Miracle-dz/UniFAR-FTUs huggingface dataset:
The composition and distribution of semi-labile dissolved organic matter across the southwest Pacific

Abstract. The distribution and dynamics of dissolved organic carbon (DOC) and dissolved combined neutral sugars (DCNS) were studied across an increasing oligotrophic gradient (18 to 22∘ S latitude) in the tropical South Pacific Ocean, spanning from the Melanesian Archipelago (MA) area to the western part of the South Pacific gyre (WGY), in austral summer as a part of the OUTPACE project. Our results show that DOC and DCNS concentrations exhibited no statistical differences between the MA and WGY areas (0–200 m: 47–81 µM C for DOC and 0.2-4.2 µM C for DCNS). However, due to a deepening of the euphotic zone, a deeper penetration of DOC was noticeable at 150 m of depth at the WGY area. Excess DOC (DOCEX) was determined as the difference between surface and deep-sea DOC values, and euphotic zone integrated stocks of both DOC and DOCEX were higher in the WGY than the MA area. Considering DOCEX as representative of semi-labile DOC (DOCSL), its residence time was calculated as the ratio of DOCSL to bacterial carbon demand (BCD). This residence time was 176±43 days (n=3) in the WGY area, about 3 times longer than in the MA area (Tr=51±13 days, n=8), suggesting an accumulation of semi-labile dissolved organic matter (DOM) in the surface waters of WGY. Average epipelagic (0–200 m) DCNS yields (DCNS × DOC−1) based on volumetric data were roughly similar in both areas, accounting for ∼2.8 % of DOC. DCNS exhibited a longer residence time in WGY (Tr=91±41 days, n=3) than in MA (Tr=31±10 days, n=8), further suggesting that this DCNS pool persists longer in the surface waters of the WGY. The accumulation of DOCEX in the surface waters of WGY is probably due to very slow bacterial degradation due to nutrient and/or energy limitation of heterotrophic prokaryotes, indicating that biologically produced DOC can be stored in the euphotic layer of the South Pacific gyre for a long period.
Unifying Hybrid Types and Contracts

Contract systems and hybrid type systems provide two alternative approaches for enforcing precisely-defined interface specifications, with complementary advantages: contract systems excel at blame assignment, whereas hybrid type systems support type-based static analysis. We unify these two approaches by demonstrating that hybrid type checking is sufficiently expressive to encode higher-order contracts with proper blame assignment. In particular, a contract obligation that enforces both sides of a contract is decomposed into two type casts that each enforce one side of the contract. This expressiveness result provides several benefits, including allowing one of these casts to be lifted from variable references to variable definitions, resulting in improved contract coverage and removing the need for privileged contract obligations.
Poststroke Depression: A Scientific Statement for Healthcare Professionals From the American Heart Association/American Stroke Association

Poststroke depression (PSD) is common, affecting approximately one third of stroke survivors at any one time after stroke. Individuals with PSD are at a higher risk for suboptimal recovery, recurrent vascular events, poor quality of life, and mortality. Although PSD is prevalent, uncertainty remains regarding predisposing risk factors and optimal strategies for prevention and treatment. This is the first scientific statement from the American Heart Association on the topic of PSD. Members of the writing group were appointed by the American Heart Association Stroke Council’s Scientific Statements Oversight Committee and the American Heart Association’s Manuscript Oversight Committee. Members were assigned topics relevant to their areas of expertise and reviewed appropriate literature, references to published clinical and epidemiology studies, clinical and public health guidelines, authoritative statements, and expert opinion. This multispecialty statement provides a comprehensive review of the current evidence and gaps in current knowledge of the epidemiology, pathophysiology, outcomes, management, and prevention of PSD, and provides implications for clinical practice.
Global and Regional Assessments of Paleosecular Variation Activity Over the Past 100 ka

We present a global compilation of paleomagnetic data spanning the past 100 ka. Sediment data comprise 61,687 declinations, 70,936 inclinations, and 69,596 relative paleointensities. Many sites are located in the northern Atlantic and western Pacific, with approximately twice as many data from the Northern Hemisphere as from the Southern Hemisphere. The 14,954 volcanic and archeomagnetic data are sparse, especially in the Southern Hemisphere. Directional and intensity information are aggregated under the paleosecular variation (PSV) index to assess occurrence of excursions over the past 100 ka. The Laschamp excursion (∼41 ka) is clearly defined across globally distributed sediment records with an average duration of 1,300 years. Regional stacks obtained using bootstrap resampling show a more pronounced Laschamp excursion in the Northern Hemisphere than in the Southern, and in the Atlantic Hemisphere compared with the Pacific. No anomalous indices occurred around the Mono Lake excursion or other periods in the bootstrap curves. This may result from low sedimentation rates, discrepancies in age scales, large age errors, and/or the lack of global character of any transitional events. These data and associated new uncertainty estimates for the sediment records provide a good foundation for global, time‐dependent, spherical harmonic field modeling for the past 100 ka.
Limit theorems for Markov processes indexed by continuous time Galton--Watson trees

We study the evolution of a particle system whose genealogy is given by a supercritical continuous time Galton--Watson tree. The particles move independently according to a Markov process and when a branching event occurs, the offspring locations depend on the position of the mother and the number of offspring. We prove a law of large numbers for the empirical measure of individuals alive at time t. This relies on a probabilistic interpretation of its intensity by mean of an auxiliary process. The latter has the same generator as the Markov process along the branches plus additional jumps, associated with branching events of accelerated rate and biased distribution. This comes from the fact that choosing an individual uniformly at time t favors lineages with more branching events and larger offspring number. The central limit theorem is considered on a special case. Several examples are developed, including applications to splitting diffusions, cellular aging, branching L\'{e}vy processes.
Incremental computation of nested relational query expressions

Efficient algorithms for incrementally computing nested query expressions do not exist. Nested query expressions are query expressions in which selection/join predicates contain subqueries. In order to respond to this problem, we propose a two-step strategy for incrementaly computing nested query expressions. In step (1), the query expression is transformed into an equivalent unnested flat query expression. In step (2), the flat query expression is incrementally computed. To support step (1), we have developed a very concise algebra-to-algebra transformation algorithm, and we have formally proved its correctness. The flat query expressions resulting from the transformation make intensive use of the relational set-difference operator. To support step (2), we present and analyze an efficient algorithm for incrementally computing set differences based on view pointer caches. When combined with existing incremental algorithms for SPJ queries, our incremental set-difference algorithm can be used to compute the unnested flat query expressions efficiently. It is important to notice that without our incremental set-difference algorithm the existing incremental algorithms for SPJ queries are useless for any query involving the set-difference operator, including queries that are not the result of unnesting nested queries.
Expression and Functional Significance of HtrA1 Loss in Endometrial Cancer

Purpose: The purpose of this study was to determine if loss of serine protease HtrA1 in endometrial cancer will promote the invasive potential of EC cell lines. Experimental design: Western blot analysis and immunohistochemistry methods were used to determine HtrA1 expression in EC cell lines and primary tumors, respectively. Migration, invasion assays and in vivo xenograft experiment were performed to compare the extent of metastasis between HtrA1 expressing and HtrA1 knocked down clones. Results: Western blot analysis of HtrA1 in 13 EC cell lines revealed complete loss of HtrA1 expression in all seven papillary serous EC cell lines. Downregulation of HtrA1 in Hec1A and Hec1B cell lines resulted in a three- to fourfold increase in the invasive potential. Exogenous expression of HtrA1 in Ark1 and Ark2 cells resulted in three- to fourfold decrease in both invasive and migration potential of these cells. There was an increased rate of metastasis to the lungs associated with HtrA1 downregulation in Hec1B cells compared to control cells with endogenous HtrA1 expression. Enhanced expression of HtrA1 in Ark2 cells resulted in significantly less tumor nodules metastasizing to the lungs compared to parental or protease deficient (SA mutant) Ark2 cells. Immunohistochemical analysis showed 57% (105/184) of primary EC tumors had low HtrA1 expression. The association of low HtrA1 expression with high-grade endometrioid tumors was statistically significant (P = 0.016). Conclusions: Collectively, these data indicate loss of HtrA1 may contribute to the aggressiveness and metastatic ability of endometrial tumors. Clin Cancer Res; 17(3); 427–36. ©2010 AACR.
A Numerical Simulation of Long-Term Sea Level Change in the East Asian Marginal Seas

ABSTRACT Kim C. -H. ; Jang C. J., and Kim M. -W. , 2018. A Numerical Simulation of Long-Term Sea Level Change in the East Asian Marginal Seas. In: Shim, J.-S. ; Chun, I. , and Lim, H.S. (eds.), Proceedings from the International Coastal Symposium (ICS) 2018 (Busan, Republic of Korea). Journal of Coastal Research, Special Issue No. 85, pp. 546–550. Coconut Creek (Florida), ISSN 0749-0208. To investigate the regional sea level rise (SLR) and its possible mechanisms in the East Asian Marginal Seas (Yellow Sea (YS), East China Sea (ECS) and Japan/East Sea (JES)) sea level variation was simulated using the global ocean-sea ice coupled model (GFDL MOM5-SIS) forced with European Centre for Medium-range Weather Forecasts reanalysis data for 58 years (1958–2015). Seasonal variation in the simulated sea level shows comparable amplitude and phase to those of the satellite altimetry for 1993–2014 in each sea region. Rates of the simulated SLR are compared with those of the reconstructed sea level (Hamlington et al., 2011) and satellite altimetry sea level: rates of SLR in the YS, ECS and JES for 1958–2009 are 2.1 mm/yr, 2.6 mm/yr, 2.1 mm/yr in the model, and 2.2 mm/yr, 1.9 mm/yr, 2.2 mm/yr in the reconstructed sea level, respectively. For 1993–2014, the SLR rates in the YS, ECS and JES are 3.8 mm/yr, 4.1 mm/yr, 2.8 mm/yr in the model, and 3.4 mm/yr, 2.6 mm/yr, 3.1 mm/yr in the satellite altimetry sea level, respectively. The regional mean sea level distribution in the model shows the SLR of 2~5 cm for 2005 to 2014 relative to the period of 1993 to 2002, which is also evident in the satellite altimetry sea level but in more localized areas. In the SLR between those two periods, model simulation reveals that non-steric sea level change was dominant in the YS, ECS and JES, which is different from the Kuroshio region where steric component was dominant. This result suggests that the recent SLR in the East Asian Marginal Seas is mainly driven by the mass convergence such as the transport changes in the shelf area.
Coexpression of SCL and GATA3 in the V2 interneurons of the developing mouse spinal cord

The differentiation of neural progenitors into the many classes of neurons that exist in the mature spinal cord is a process that relies heavily on the activation of precise combinations of transcription factors. Defining these transcription factor combinations is an important aspect of research in developmental neurobiology that promises to provide incredible insights into the structure, function, and pathology of the central nervous system. The present study aimed to investigate a possible role for the Stem Cell Leukemia (SCL) gene, a basic helix‐loop‐helix (bHLH) transcription factor gene, in the specification of a population of neural cells in the ventral neural tube. Section RNA in situ hybridisation revealed that SCL is transiently expressed within the V2 postmitotic domain of the developing mouse spinal cord between 10.5 and 13.5 days post coitum. Double‐immunofluorescence experiments were subsequently carried out to directly compare the expression of SCL with other V2‐specific markers at the cellular level. These experiments revealed that SCL is expressed in a medially restricted subpopulation of GATA‐3 producing cells, suggesting a possible role for this factor in the differentiation of the GATA population of V2 interneurons. © 2002 Wiley‐Liss, Inc.
Decoding properties of tRNA leave a detectable signal in codon usage bias

Motivation: The standard genetic code translates 61 codons into 20 amino acids using fewer than 61 transfer RNAs (tRNAs). This is possible because of the tRNA's ability to ‘wobble’ at the third base to decode more than one codon. Although the anticodon–codon mapping of tRNA to mRNA is a prerequisite for certain codon usage indices and can contribute to the understanding of the evolution of alternative genetic codes, it is usually not determined experimentally because such assays are prohibitively expensive and elaborate. Instead, the codon reading is approximated from theoretical inferences of nucleotide binding, the wobble rules. Unfortunately, these rules fail to capture all of the nuances of codon reading. This study addresses the codon reading properties of tRNAs and their evolutionary impact on codon usage bias. Results: Using three different computational methods, the signal of tRNA decoding in codon usage bias is identified. The predictions by the methods generally agree with each other and compare well with experimental evidence of codon reading. This analysis suggests a revised codon reading for cytosolic tRNA in the yeast genome (Saccharomyces cerevisiae) that is more accurate than the common assignment by wobble rules. The results confirm the earlier observation that the wobble rules are not sufficient for a complete description of codon reading, because they depend on genome-specific factors. The computational methods presented here are applicable to any fully sequenced genome. Availability: By request from the author. Contact: alexander.roth@isb-sib.ch
Antibacterial activity of bladder surface mucin duplicated in the rabbit bladder by exogenous glycosaminoglycan (sodium pentosanpolysulfate)

Previous data from our laboratory suggest that the transitional epithelium of the urinary bladder secretes and binds to its surface a glycosaminoglycan. The presence of this substance at the bladder surface markedly reduces the ability of microorganisms to adhere to the mucosa. Furthermore, this glycosaminoglycan can be removed (with acid) and replaced by intravesical instillation of a synthetic sulfonated glycosaminoglycan (heparin), whose presence is as effective as that of the natural glycosaminoglycan in reducing adherence. We conducted the current study with a different sulfonated glycosaminoglycan to determine whether the antiadherence activity is generalized to heparin congeners and whether the antiadherence effect of heparin is independent of its known anticoagulant activity. In this study we examined the sulfonated glycosaminoglycan, sodium pentosanpolysulfate, which lacks significant anticoagulant activity, and found it to have a mechanism of antiadherence analogous to that of heparin and almost equally as active on a weight basis.
Function and regulation of FoxF1 during Xenopus gut development

Development of the visceral mesoderm is a critical process in the organogenesis of the gut. Elucidation of function and regulation of genes involved in the development of visceral mesoderm is therefore essential for an understanding of gut organogenesis. One of the genes specifically expressed in the lateral plate mesoderm, and later in its derivative, the visceral mesoderm, is the Fox gene FoxF1. Its function is critical for Xenopus gut development, and embryos injected with FoxF1 morpholino display abnormal gut development. In the absence of FoxF1 function, the lateral plate mesoderm, and later the visceral mesoderm, does not proliferate and differentiate properly. Region- and stage-specific markers of visceral mesoderm differentiation, such as Xbap and α-smooth muscle actin, are not activated. The gut does not elongate and coil. These experiments provide support for the function of FoxF1 in the development of visceral mesoderm and the organogenesis of the gut. At the molecular level, FoxF1 is a downstream target of BMP4 signaling. BMP4 can activate FoxF1 transcription in animal caps and overexpression of FoxF1 can rescue twinning phenotypes, which results from the elimination of BMP4 signaling. The cis-regulatory elements of FoxF1 are located within a 2 kb DNA fragment upstream of the coding region. These sequences can drive correct temporal-spatial expression of a GFP reporter gene in transgenic Xenopus tadpoles. These sequences represent a unique tool, which can be used to specifically alter gene expression in the lateral plate mesoderm.
Complete Genome of the Broad-Host-Range Erwinia amylovora Phage ΦEa21-4 and Its Relationship to Salmonella Phage Felix O1

ABSTRACT The first complete genome sequence for a myoviridal bacteriophage, ΦEa21-4, infecting Erwinia amylovora, Erwinia pyrifoliae, and Pantoea agglomerans strains has been determined. The unique sequence of this terminally redundant, circularly permuted genome is 84,576 bp. The ΦEa21-4 genome has a GC content of 43.8% and contains 117 putative protein-coding genes and 26 tRNA genes. ΦEa21-4 is the first phage in which a precisely conserved rho-independent terminator has been found dispersed throughout the genome, with 24 copies in all. Also notable in the ΦEa21-4 genome are the presence of tRNAs with six- and nine-base anticodon loops, the absence of a small packaging terminase subunit, and the presence of nadV, a principle component of the NAD+ salvage pathway, which has been found in only a few phage genomes to date. ΦEa21-4 is the first reported Felix O1-like phage genome; 56% of the predicted ΦEa21-4 proteins share homology with those of the Salmonella phage. Apart from this similarity to Felix O1, the ΦEa21-4 genome appears to be substantially different, both globally and locally, from previously reported sequences. A total of 43 of the 117 genes are unique to ΦEa21-4, and 32 of the Felix O1-like genes do not appear in any phage genome sequences other than ΦEa21-4 and Felix O1. N-terminal sequencing and matrix-assisted laser desorption ionization-time of flight analysis resulted in the identification of five ΦEa21-4 genes coding for virion structural proteins, including the major capsid protein.
Knowing What’s Out There: Awareness of Non-Alcoholic Fatty Liver Disease

Background: Non-alcoholic fatty liver disease (NAFLD) is the most common hepatic disorder, which poses a significant health burden in the western countries. As the epidemic of obesity slides health downward, the incidence of NAFLD is evidently increasing. Aim: We aimed to ascertain the awareness of NAFLD and its risk factors in the general population, which may be helpful in designing educational tools to promote prevention, early detection, and treatment of this disorder. Methods: A survey of 5000 non-institutionalized residents of Brooklyn, NY, USA was conducted. Sixteen items were included in the survey questionnaire including awareness of fatty liver, predisposing factors of NAFLD, awareness of cirrhosis, and conditions that advance to cirrhosis. The questionnaire also addressed awareness of prevention, diagnostic methods and treatment of NAFLD, and education of physicians to their patients about NAFLD. Results: Overwhelming majority of the subjects was not aware of NAFLD and stated that their physicians did not have a discussion about NAFLD. Conclusion: Non-alcoholic fatty liver disease is a preventable liver disorder with limited treatment options. Thorough counseling by primary care physicians can be of paramount importance in preventive strategy for NAFLD. We should target our teenage population in an era of obesity epidemics of all times.
A cloud on the horizon: the challenge of developing applications for Android and iPhone

In the last few years, since the initial release of Android and iPhone in 2007, building applications for mobile platforms has opened many new possibilities for software developers. Development for mobile devices comes with its own challenges like battery life, small screens and touch screen interface. This paper goes into detail on some of the challenges when developing for Android and iOS devices.
Generative Emergence: A New Discipline of Organizational, Entrepreneurial, and Social Innovation

Chapter 1. Why Emergence Chapter 2. Prototypes of Emergence Chapter 3. Methods for Studying Emergence - 15 Fields of Complexity Science Chapter 4. Defining Emergence and Generative Emergence Chapter 5. Types of Emergence Studies Chapter 6. Dissipative Structures Chapter 7. Applications to Organizations Chapter 8. Introducing Dynamic States Chapter 9. Outcomes of Generative Emergence Chapter 10. Introducing the Five-Phase Process Model Of Generative Emergence Chapter 11. Phase 2 - Stress & Experiments Chapter 12. Phase 3 - Amplification and Critical Events Chapter 13. Phase 4 - New Order through Recombination Chapter 14. Phase 5 - Stabilizing Feedback Chapter 15. Cycles of Emergence Chapter 16. Cycles of Re-Emergence Chapter 17. Boundaries of Emergence, and Beyond the Boundaries Chapter 18. Enacting Emergence
Paleo-environment and provenance in a lacustrine shallow-water delta-meandering river sedimentary system: insights from the Middle–Upper Jurassic formations of the Fukang Sag of Junggar Basin, NW China

Abstract The Middle–Upper Jurassic Shishugou Group in the central Junggar Basin was deposited in a lacustrine shallow-water delta-meandering river sedimentary system. The integrated petrological (thin-section, granularity and heavy minerals analysis), geochemical (trace elements and rare earth elements analysis) and geophysical analyses (well logging and 3D-seismic slice analysis) are used to determine redox conditions, paleoclimate, paleosalinity, provenance and sedimentary evolution extant during deposition of the Shishugou Group: (1) the redox condition changed from a weak anoxic/oxic condition to a strongly oxic condition; (2) the climate changed from humid to hot and arid in the Middle–Late Jurassic, which may have resulted in the lake water having slight–medium salinity; (3) the relatively distant northeastern provenance from the Kelameili Mountain is the most important sediment source; and (4) the south provenance from the Tianshan Mountains (Bogeda Shan) decreases with the development of the sag piedmont, which supplies sediments to the southeastern Fukang Sag. The sedimentary environment changed from a lacustrine shallow-water delta to a meandering river during the deposition of the Shishugou Group. The shallow-water meandering river delta was characterised by pervasive mudstones with oxide colours, thin single-layer sand bodies (1–15 m, mean 3 m), relatively low sand–strata ratios (0.2–0.5) and the absence of progradation, mouth bars and reverse rhythms. The gentle slope is the primary condition necessary for the formation of a shallow-water meandering river delta. Paleo-environment (climate change from warm-humid to hot-arid) and the stable and remote Kelameili Mountain provenance played critical roles in the development and evolution of lacustrine–delta-meandering river sedimentary systems.