Miracle-dz/UniFAR-FTUs huggingface dataset:
Capturing dynamics of marine inorganic carbon fluxes from diurnal to decadal timescales

The marine carbon cycle plays an important role in regulating Earth's climate. The vastness of the open ocean and the large variability in the coastal ocean provide obstacles to accurately quantify storage and transport of inorganic carbon within marine ecosystems and between marine and other earth systems. Thus far, the open ocean has been the only true net sink of anthropogenic carbon dioxide (Catro) emissions. However, ocean storage of CItII(, is not uniformly distributed. Changes in water chemistry in the Northeast Pacific were quantified to estimate the amount of Cantiro stored in this region over the last decade. This additional Ca.thro was found to cause acidification and aragonite saturation horizon shoaling at rates towards the higher end of those found in Pacific and Atlantic Ocean basins, making the Northeast Pacific one of the most sensitive regions to the invasion of anthropogenic carbon dioxide. Due to large variability in biogeochemical signals in coastal oceans, it is challenging to accurately assess carbon fluxes across different boundaries, such as tidal exchange between coastal wetlands and coastal oceans. Coastal salt marshes have been suggested to be a large net CO 2 sink, thus designated as a type of "blue carbon." However, accurate and dynamic estimates of carbon fluxes to and from tidal marshes are still premature, particularly carbon fluxes from marshes to the coastal ocean via tidal exchange, often referred to as marsh lateral fluxes. In this thesis, lateral total alkalinity (TA) and dissolved inorganic carbon (DIC) export fluxes were realistically quantified using high frequency time-series, in situ data. High-resolution fluxes permitted a closer look at how marsh generated TA and DIC are being exported over diurnal, spring-neap, and seasonal scales. I investigated the best way to capture variability of marsh exports via traditional bottle sampling and assessed uncertainties associated with different sampling strategies. Marsh TA and DIC exports significantly modified buffering capacity of coastal waters. This work contains the first realistic estimate of TA exports from a tidal salt marsh. Accurate estimates of DIC and TA fluxes indicate the significance of salt marshes to the coastal carbon and alkalinity budgets. Thesis supervisor: Zhaohui Aleck Wang Title: Associate Scientist, Woods Hole Oceanographic Institution
Reduced-Dose or Discontinuation of Bevacizumab Might Be Considered after Variceal Bleeding in Patients with Hepatocellular Carcinoma Receiving Atezolizumab/Bevacizumab: Case Reports

Background and Objectives: Variceal bleeding (VB) is the most concerning condition that is difficult to treat after atezolizumab/bevacizumab in patients with advanced hepatocellular carcinoma (HCC). Materials and Methods: We would like to introduce the cases of two patients who underwent bevacizumab reduction or discontinuation when VB occurred after atezolizumab/bevacizumab. Results: VB occurred in two patients who showed good tumor response after atezolizumab/bevacizumab treatment, and all VBs were successfully treated with endoscopic variceal ligations. In the first patient, VB did not occur as the tumor response decreased after a 50% reduction in bevacizumab. In the second patient, VB occurred again after a 50% bevacizumab reduction, so bevacizumab was discontinued and treatment with atezolizumab alone has been successfully maintained. Conclusions: Accordingly, we would like to suggest that considering bevacizumab dose reduction instead of changing to tyrosine kinase inhibitor may be a good clinical choice in atezolizumab/bevacizumab patients who develop VB.
Coastal bluffs of New England

Although its shoreline differs in many ways from that of the mid-Atlantic and southeastern states, New England is part of the United States East Coast passive continental margin. South of New England, the outer coast of the United States is dominated by barrier islands, but bedrock frames all of the coast north of New York City with the exception of Cape Cod and nearby islands. The rocks of this region are all part of the Appalachian Mountains, which formed primarily during several plate collisions in the early-middle Paleozoic Era. North America grew as a consequence of these collisions, and the rocks of the New England coast are a patchwork of exotic terranes derived from a variety of sources. Following the initial formation of the Appalachians, several basins within them filled with sedimentary rocks in the late Paleozoic. The Atlantic Ocean opened up in the early Mesozoic and failed rift basins, filled with sandstones and basaltic volcanic rocks, remain along the coast and offshore from that time. The last igneous rocks formed in the late Mesozoic, and the region has generally undergone erosion since then. The weathered products of the erosion of the Appalachian Mountains, the coastal plain sediments of the south, are not exposed on the New England coast, and were presumably eroded themselves. It is not a coincidence that the latest agents of erosion, continental glaciers, covered all of New England, and reached only as far south as Long Island, New York. Although the glaciers removed the Coastal Plain material, they left in its place a heterogeneous assemblage of deposits partly mantling the bedrock. Contemporary reworking of these glacial deposits by coastal processes provides materials for the highly variable modern environments of the New England coastal zone. The irregular shape of the New England coast is mostly due to the structure and differential erosion of its bedrock skeleton. Rocks that have most resisted erosion by glaciers (igneous rocks, quartzites) tend to form peninsulas, islands, and relatively high headlands. More easily eroded rocks (sedimentary rocks and slates/shists) underlie embayments and estuaries. Because these rock types are associated with numerous exotic terranes, and often separated by ancient fault zones, there is great variation in topography and shoreline orientation throughout New England (fig. 1). Despite this overall heterogeneity, the coast may simply be described as a series of bedrock compartments that are internally relatively homogeneous, but distinct from their neighbors (fig. 1). Extending southwest from the Bay of Fundy, Canada, the cliffed coastline (fig. 1) is framed by fault zones, and is a relatively high-relief shoreline of igneous rocks with few embayments (Kelley, 1987, 1993; Kelley and others, 1989, 1995, 2003). As a result of the high rock cliffs, bluffs of unconsolidated sediment are relatively rare. Coastal Bluffs of New England
Factors Associated with 5-year Risk of Hip Fracture in Postmenopausal Women

T HE ESTIMATED 329 000 HIP fractures that occur annually in the United States 1 are associated with high morbidity, mortality , and cost. 2 Prevention of hip fracture is a high priority for patients, physicians, and public health. Several studies and consensus opinions have investigated the risk factors for hip fractures. 3-8 The Study of Osteoporotic Fractures (SOF), 3 which included 7782 women over 5 years, set the benchmark for establishing risk of hip fracture to date. The number of women included in the Women's Health Initiative (WHI) is an order of magnitude larger than SOF, and WHI includes nearly 20% minority women. Although dual-energy x-ray absorp-tiometry (DXA) scan can precisely predict risk of hip fractures, as it did for a small subset of women participating in WHI, by assessing bone mineral density (BMD), clinicians and patients would benefit from assessing risk by Context The 329 000 hip fractures that annually occur in the United States are associated with high morbidity, mortality, and cost. Identification of those at high risk is a step toward prevention. Objective To develop an algorithm to predict the 5-year risk of hip fracture in post-menopausal women. Design, Setting, and Participants A total of 93 676 women who participated in the observational component of the Women's Health Initiative (WHI), a multiethnic longitudinal study, were used to develop a predictive algorithm based on commonly available clinical features. Selected factors that predicted hip fracture were then validated by 68 132 women who participated in the clinical trial. The model was tested in a subset of 10 750 women who had undergone dual-energy x-ray absorptiometry (DXA) scans for bone mass density assessment. Main Outcome Measure The prediction of centrally adjudicated hip fracture, measured by the area under the receiver operator characteristic (ROC) curves. Results During a mean (SD) follow-up of 7.6 (1.7) years, 1132 hip fractures were identified among women participating in the observational study (annualized rate, 0.16%), whereas during a mean follow-up of 8.0 (1.7) years, 791 hip fractures occurred among women participating in the clinical trial (annualized rate, 0.14%). Eleven factors predicted hip fracture within 5 years: age, self-reported health, weight, height, race/ethnicity, self-reported physical activity, history of fracture after age 54 years, parental hip fracture, current smoking, current corticosteroid use, and treated diabetes. Receiver operating characteristic curves showed that the algorithm had an area under the curve of 80% (95% confidence interval [CI], 0.77%-0.82%) when …
Capstone Project : Proposal for an Open Source Implementation of V-OXT , a Scalable Verifiable Encrypted Search Protocol

In recent decades a number of factors have made the outsourcing of the storage of digital information to “the cloud” indispensable. The growth of the personal computer industry, the rise of the smart-phone, the advent of “big data”, the need to persist data to avoid its loss in the event of a hardware failure, and the large scale use of the Internet have all contributed to the trend—increasingly, data is stored not on the hard drives of personal computers but in specialized data warehouses (the cloud) which offer global access via the Internet, resiliency to hardware failure, and cheap storage. The use of the cloud brings with it special security concerns. Most notably, user data should not, under any circumstances, become accessible to others. One solution for this problem is the encryption of all data in the cloud and, while this is an effective way to keep data safe from malicious data warehouse operator or a security breach, it does not allow for partial access of data, i.e. data owners must download entire files to search through them. Experimental implementations for searchable symmetric encryption (SSE) that are both secure and scalable exist, but they do not offer protection from malicious servers. Our proposed project is an improvement on the OXT protocol developed by Cash, et al.[1] that does not rely on the assumption that the server storing the data is “honest”. Clients using the proposed system will be able to store and search through vast collections of their documents without risking the compromise of their data in the event of security breach. 1 Motivation and Benefits to the Community The primary benefit of this project is that it makes the outsourcing of data storage (a growing industry trend) secure and easy. Data storage providers are a dime a dozen on the open Internet today. On-line cloud services such as DropBox and Google Drive are explicitly used by millions of people to store every day data on the cloud. Furthermore, services like email and Facebook (used by billions) provide implicit data storage, with files such as photos stored as part
LocalMotif - An In-Silico Tool for Detecting Localized Motifs in Regulatory Sequences

In silico motif finding algorithms are often used for discovering protein-DNA binding sites in a set of regulatory sequences. Current algorithms mainly address motif discovery in short sequences. Analyzing long sequences can be quite challenging not only due to increasing time and memory requirements of the algorithm, but also decreasing accuracy. However, in case the motif is localized in a short interval of the long sequences relative to an anchor point, it is tenable to detect it easily by restricting the search to that interval. But the region of localization of the motif is not known a priori. This paper reports an algorithm called LocalMotif to detect localized motifs in long regulatory sequences. A novel score function predicts the region of localization of the motif. This score is combined with other scoring measures including Z-score and relative entropy to detect the motif. The algorithm is optimized for fast processing of long regulatory sequences. Tests on simulated and real datasets confirm that LocalMotif accurately determines the region of localization of motifs and automatically discovers the biologically relevant motifs, which can be detected by other motif finding algorithms only when the search is restricted to the relevant interval
Joint English Spelling Error Correction and POS Tagging for Language Learners Writing

We propose an approach to correcting spelling errors and assigning part-of-speech (POS) tags simultaneously for sentences written by learners of English as a second language (ESL). In ESL writing, there are several types of errors such as preposition, determiner, verb, noun, and spelling errors. Spelling errors often interfere with POS tagging and syntactic parsing, which makes other error detection and correction tasks very difficult. In studies of grammatical error detection and correction in ESL writing, spelling correction has been regarded as a preprocessing step in a pipeline. However, several types of spelling errors in ESL are difficult to correct in the preprocessing, for example, homophones (e.g. *hear/here), confusion (*quiet/quite), split (*now a day/nowadays), merge (*swimingpool/swimming pool), inflection (*please/pleased) and derivation (*badly/bad), where the incorrect word is actually in the vocabulary and grammatical information is needed to disambiguate. In order to correct these spelling errors, and also typical typographical errors (*begginning/beginning), we propose a joint analysis of POS tagging and spelling error correction with a CRF (Conditional Random Field)-based model. We present an approach that achieves significantly better accuracies for both POS tagging and spelling correction, compared to existing approaches using either individual or pipeline analysis. We also show that the joint model can deal with novel types of misspelling in ESL writing.
One/T-Time Signatures Using Self-Certified Public Keys

One-time signature schemes (OTSS) are based on efficient one-way functions. They achieve fast signing and verification, and sign the message at most 1 time. OTSSs are used to replace asymmetric signatures that incur highercosts in cases where performance is critical. For example, OTSSs are employed in chip cards where low computation complexity is required. The secret key and public key of an OTSS are used only once; this creates a problem when we use a certificate-based public key system with the OTSS since the public key certification will cause the certification authority CA to offer public key evidence to the signer every time the OTSS is used. It appears that this evidence is unnecessary and impractical. In this paper, we discuss the certificate problems faced in the OTSS public key system. In our proposed scheme based on the self-certified public key system, it is recess any to contact the CA only 1 time and only 1 certificate needs to be obtained from the CA. The communication costs of the signer and CA are greatly reduced as comparing to that in case of the tree-authentication-based scheme proposed by Merkle [6].
A Two-Phase Case-Control Study of Autism Risk Among Children Born From the Late 1990s Through the Early 2000s in the United States

Background This study evaluated the hypothesis that the 1999 recommendation by the American Academy of Pediatrics (AAP) and US Public Health Service (PHS) to reduce exposure to mercury (Hg) from Thimerosal in US vaccines would be associated with a reduction in the long-term risk of being diagnosed with autism. Material/Methods A two-phase assessment utilizing a case (n=73) -control (n=11,783) study in the Vaccine Adverse Event Reporting System (VAERS) database (for hypothesis generating) and a more rigorous, independent matched case (n=40) -control (n=40) study (hypothesis testing) was undertaken. Results Analysis of the VAERS database using logistic regression revealed that the odds ratio (OR) for being an autism case in the VAERS database significantly decreased with a more recent year of vaccination in comparison to controls (OR=0.65) from 1998 to 2003. Sex-separated analyses revealed similar significant effects for males (OR=0.62) and females (OR=0.71). Analyses of the matched case-control data revealed, using the t-test statistic, that the mean date of birth among cases diagnosed with an autism spectrum disorder (ASD) (2000.5±1.2) was significantly more in the past than in controls (2001.1±1.3). Logistic regression also revealed that the OR for being diagnosed with ASD significantly decreased with a more recent date of birth in comparison to controls (OR=0.67) from 1998–2003. Conclusions This study reveals that the risk of autism during from the late1990s to early 2000s in the US significantly decreased with reductions in Hg exposure from Thimerosal-containing childhood vaccines, but future studies should examine this phenomenon in other US populations. Vaccine programs have significantly reduced the morbidity and mortality associated with infectious disease, but Thimerosal should be removed from all vaccines.
An All-Around Near-Optimal Solution for the Classic Bin Packing Problem

In this paper we present the first algorithm with optimal average-case and close-to-best known worst-case performance for the classic on-line problem of bin packing. It has long been observed that known bin packing algorithms with optimal average-case performance were not optimal in the worst-case sense. In particular First Fit and Best Fit had optimal average-case ratio of 1 but a worst-case competitive ratio of 1.7. The wasted space of First Fit and Best Fit for a uniform random sequence of length $n$ is expected to be $\Theta(n^{2/3})$ and $\Theta(\sqrt{n} \log ^{3/4} n)$, respectively. The competitive ratio can be improved to 1.691 using the Harmonic algorithm; further variations of this algorithm can push down the competitive ratio to 1.588. However, Harmonic and its variations have poor performance on average; in particular, Harmonic has average-case ratio of around 1.27. In this paper, first we introduce a simple algorithm which we term Harmonic Match. This algorithm performs as well as Best Fit on average, i.e., it has an average-case ratio of 1 and expected wasted space of $\Theta(\sqrt{n} \log ^{3/4} n)$. Moreover, the competitive ratio of the algorithm is as good as Harmonic, i.e., it converges to $ 1.691$ which is an improvement over 1.7 of Best Fit and First Fit. We also introduce a different algorithm, termed as Refined Harmonic Match, which achieves an improved competitive ratio of $1.636$ while maintaining the good average-case performance of Harmonic Match and Best Fit. Finally, our extensive experimental evaluation of the studied bin packing algorithms shows that our proposed algorithms have comparable average-case performance with Best Fit and First Fit, and this holds also for sequences that follow distributions other than the uniform distribution.
Information Fusion for Answering Factoid Questions

We describe an experiment involving reranking a set of answer extractions for where- questions based on computing equivalence and inclusion relations among a question and its set of answer extractions. The purpose of automated Question Answering (QA) is to retrieve an answer to a question expressed in natural language. Whereas Information Retrieval provides a set of documents covering the topic expressed by a keyword query, QA focuses on retrieving ne-grained and exact answers. The Text REtrieval Conference (TREC), organised each year by NIST, has oered since 1999 a specic track to evaluate large-scale open-domain QA systems. For TREC 2003, three kinds of questions were distinguished: fac- toid, denition and list questions. While the rst type expects only one exact answer, the latter two require an advanced analysis of the potential answer space to evaluate which potential answers t the expected denition (\What are fractals? ") or are part of the answer list (\Who were the great opera tenors of the twentieth century? "). Providing multiple answers is challenging, espe- cially when the source of such answers is untyped and heterogeneous free text. In this context, we are developing a new technique based on information fusion to allow answer comparison and improve answer selection. The main use of in- formation fusion in language technology has so far been in summarisation, to organize information coming from heterogeneous sources. Here we show that
Bimolecular Complementation to Visualize Filovirus VP40-Host Complexes in Live Mammalian Cells: Toward the Identification of Budding Inhibitors

Virus-host interactions play key roles in promoting efficient egress of many RNA viruses, including Ebola virus (EBOV or “e”) and Marburg virus (MARV or “m”). Late- (L-) domains conserved in viral matrix proteins recruit specific host proteins, such as Tsg101 and Nedd4, to facilitate the budding process. These interactions serve as attractive targets for the development of broad-spectrum budding inhibitors. A major gap still exists in our understanding of the mechanism of filovirus budding due to the difficulty in detecting virus-host complexes and mapping their trafficking patterns in the natural environment of the cell. To address this gap, we used a bimolecular complementation (BiMC) approach to detect, localize, and follow the trafficking patterns of eVP40-Tsg101 complexes in live mammalian cells. In addition, we used the BiMC approach along with a VLP budding assay to test small molecule inhibitors identified by in silico screening for their ability to block eVP40 PTAP-mediated interactions with Tsg101 and subsequent budding of eVP40 VLPs. We demonstrated the potential broad spectrum activity of a lead candidate inhibitor by demonstrating its ability to block PTAP-dependent binding of HIV-1 Gag to Tsg101 and subsequent egress of HIV-1 Gag VLPs.
Asynchronous Rendering of Time-Variant Volumes with Workload-Based Data Shuffling

Complex time-varying phenomena usually produce volume datasets that are not static but dynamic in time. The amounts of storage and the computing power needed to visualize such datasets can easily exceed what could be offered by a single processor. Therefore, networks of computers are ideal to render them. However, data distribution schemes can be highly vulnerable to how the user wants to visualize the data, which could be stored in bricks that have several levels of resolutions. This scenario is highly influenced by the error estimates that low resolution data accumulate to represent high resolution data. Different set of error tolerances can produce rendering sequences that make the workload of processors imbalance. We present the asynchronous rendering of time-variant volume datasets under a shuffled distribution, which is based on the expected number of bricks to render. The data is subdivided into partitions that hold many bricks; a metric is then calculated for every partition. The partitions are then mapped to processors based on the metric, so that high concentration of bricks go where low concentration have been previously assigned; and vice versa. Because of this behavior, asynchronous rendering is required; otherwise, processors stand idle instead of rendering frames. Our results compare our method against the traditional synchronous rendering found in most of the parallel rendering literature. In all cases, our method balances the workload better in terms of number of bricks.