bluuebunny/crossref_metadata_2025_split huggingface dataset:
OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
Authors: Sethna Zachary , Elhanati Yuval , Callan Curtis G , Walczak Aleksandra M , Mora Thierry 
Published: January 2019

Abstract

Motivation
High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the correct amino acid translation is computationally intractable. The purpose of this paper is to present a solution to this problem.

Results
We use dynamic programming to construct an efficient and flexible algorithm, called OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid sequences), for calculating the probability of generating a given CDR3 amino acid sequence or motif, with or without V/J restriction, as a result of V(D)J recombination in B or T cells. We apply it to databases of epitope-specific T-cell receptors to evaluate the probability that a typical human subject will possess T cells responsive to specific disease-associated epitopes. The model prediction shows an excellent agreement with published data. We suggest that OLGA may be a useful tool to guide vaccine design.

Availability and implementation
Source code is available at https://github.com/zsethna/OLGA.

Supplementary information
Supplementary data are available at Bioinformatics online.
A Method to Bound the Number of Active S-Boxes for a Kind of AES-Like Structure
Authors: Wang Qian , Jin Chenhui 
Published: January 2019

AbstractDue to the strong security and high performance of the AES block cipher, many hash functions take AES-like structures as building blocks. To evaluate the security of these AES-like structures against differential cryptanalysis, giving the lower bounds on the number of active S-boxes in a differential trail, is an important perspective. However, the original ‘wide-trail strategy’ for AES becomes less effective to get tight bounds for these AES-like structures, because of the different state dimensions (M×M2, instead of M×M) and different round functions from AES. In this paper, we focus on a kind of AES-like structure with state dimensions M×M2, diffusion-optimal permutations and MixColumns transformations using MDS matrices. Inspired by the ‘wide-trail strategy’, we propose a theoretical method to count active S-boxes, by which we prove that there are at least rBd(Bd−1) active S-boxes in any 2r(r≥3) rounds of such an AES-like structure, where Bd is the differential branch number of the MixColumns transformation and equals to M+1. What’s more, this lower bound can be achieved by some diffusion layers. As examples, we apply our method to the LANE hash function and 3D block cipher, optimal lower bounds are both got.
Variety Is the Spice of Late Life: Social Integration and Daily Activity
Authors: Fingerman Karen L , Huo Meng , Charles Susan T , Umberson Debra J 
Published: January 2019

Abstract

Objectives
Social integration (involvement with a diverse array of social ties) has been linked to positive outcomes including better physical health. Research has not investigated whether encounters with diverse social ties enhance individuals’ daily behaviors. The objectives of this study were to assess whether social ties connect individuals to more diverse daily behaviors, physical activity, and nonsedentary time as well as more positive mood.

Method
Older adults (aged 65+, n = 313) provided information about their 10 closest social ties. Then they completed ecological momentary assessment (EMA) surveys every 3 hr for 5–6 days where they reported on social encounters and behaviors. They also wore Actical accelerometers to objectively measure physical activity.

Results
Multilevel models revealed that encounters with a greater variety of social ties was associated with engaging in a greater variety of behaviors, more objectively measured physical activity, and a smaller proportion of time spent sedentary. Encounters with weak ties/peripheral social ties accounted for this increased activity (compared to being alone or with close friends or family). Moreover, involvement with diverse ties or diverse behaviors was associated with better mood.

Discussion
Findings are discussed in terms of social engagement theory, network diversity, and the benefits of weak ties.
Shear wave imaging to determine near-borehole faults for ocean drilling
exploration
Authors: Lee Sheng-Qing , Tang Xiao-Ming , Su Yuan-da 
Published: January 2019

SUMMARY
The Deep Sea Drilling Project (DSDP) or Ocean Drilling Program (ODP), and the recent International Discovery Program (IODP) usually acquire borehole geophysical data for planetary exploration. A recently developed shear wave imaging technique was applied to the acoustic waveform log data of the IODP U1473A hole to image a fault system about 40 m away from the borehole. The shear wave imaging not only allowed us to delineate the fault structure in the vicinity of the borehole, but also to determine the orientation of the fault system, providing much needed information for the interpretation of the tectonic situation of the well site. Theory and method for the imaging application are elaborated and data processing results are presented along with the supporting borehole geophysical data. Its successful application to the IODP U1473A hole suggests that the shear wave imaging technique can be applied to the previously recorded and future ODP/IOPD borehole acoustic data, promising the extraction of valuable geophysical and geological information.
Ensemble models for data-poor assessment: accounting for uncertainty in life-history information
Authors: Rudd Merrill B , Thorson James T , Sagarese Skyler R 
Published: January 2019

AbstractLength measurements from fishery catch can be used in data-limited assessments to estimate important population parameters to guide management, but results are highly sensitive to assumptions about biological information. Ideally, local life history studies inform biological parameters. In the absence of reliable local estimates, scientists and managers face the difficult task of agreeing on fixed values for life-history parameters, often leading to additional uncertainty unquantified in the assessment or indecision defaulting to status-quo management. We propose an ensemble approach for incorporating life history uncertainty into data-limited stock assessments. We develop multivariate distributions of growth, mortality, and maturity parameter values, then use bivariate interpolation and stacking as an ensemble learning algorithm to propagate uncertainty into length-based, data-limited stock assessment models. Simulation testing demonstrated that stacking across life history parameter values leads to improved interval coverage over simple model averaging or assuming the parameter distribution means when the true life-history parameter values are unknown. We then applied the stacking approach for a U.S. Caribbean stock where the Scientific and Statistical Committee did not accept the assessment due to uncertainty in life history parameters. Stacking can better characterize uncertainty in stock status whenever life-history parameters are unknown but likely parameter distributions are available.
Symplectic Geometry of a Moduli Space of Framed Higgs Bundles
Authors: Biswas Indranil , Logares Marina , Peón-Nieto Ana 
Published: January 2019

Abstract
Let $X$ be a compact connected Riemann surface and $D$ an effective divisor on $X$. Let ${\mathcal N}_H(r,d)$ denote the moduli space of $D$-twisted stable Higgs bundles (a special class of Hitchin pairs) on $X$ of rank $r$ and degree $d$. It is known that ${\mathcal N}_H(r,d)$ has a natural holomorphic Poisson structure that is in fact symplectic if and only if $D$ is the zero divisor. We prove that ${\mathcal N}_H(r,d)$ admits a natural enhancement to a holomorphic symplectic manifold that is called here as ${\mathcal M}_H(r,d)$. This ${\mathcal M}_H(r,d)$ is constructed by trivializing, over $D$, the restriction of the vector bundles underlying the $D$-twisted Higgs bundles; such objects are called here as framed Higgs bundles. We also investigate the symplectic structure on the moduli space ${\mathcal M}_H(r,d)$ of framed Higgs bundles as well as the Hitchin system associated to it.
Estimating the impact of deploying an electronic clinical decision support tool as part of a national practice improvement project
Authors: Kerns Ellen K , Staggs Vincent S , Fouquet Sarah D , McCulloh Russell J 
Published: January 2019

Abstract

Objective
Estimate the impact on clinical practice of using a mobile device–based electronic clinical decision support (mECDS) tool within a national standardization project.

Materials and Methods
An mECDS tool (app) was released as part of a change package to provide febrile infant management guidance to clinicians. App usage was analyzed using 2 measures: metric hits per case (metric-related screen view count divided by site-reported febrile infant cases in each designated market area [DMA] monthly) and cumulative prior metric hits per site (DMA metric hits summed from study month 1 until the month preceding the index, divided by sites in the DMA). For each metric, a mixed logistic regression model was fit to model site performance as a function of app usage.

Results
An increase of 200 cumulative prior metric hits per site was associated with increased odds of adherence to 3 metrics: appropriate admission (odds ratio [OR], 1.12; 95% confidence interval [CI], 1.06-1.18), appropriate length of stay (OR, 1.20; 95% CI, 1.12-1.28), and inappropriate chest x-ray (OR, 0.82; 95% CI, 0.75-0.91). Ten additional metric hits per case were also associated: OR were 1.18 (95% CI, 1.02-1.36), 1.36 (95% CI, 1.14-1.62), and 0.74 (95% CI, 0.62-0.89).

Discussion
mECDS tools are increasingly being implemented, but their impact on clinical practice is poorly described. To our knowledge, although ecologic in nature, this report is the first to link clinical practice to mECDS use on a national scale and outside of an electronic health record.

Conclusions
mECDS use was associated with changes in adherence to targeted metrics. Future studies should seek to link mECDS usage more directly to clinical practice and assess other site-level factors.
Data linkages between patient-powered research networks and health plans: a foundation for collaborative research
Authors: Agiro Abiy , Chen Xiaoxue , Eshete Biruk , Sutphen Rebecca , Bourquardez Clark Elizabeth , Burroughs Cristina M , Nowell W Benjamin , Curtis Jeffrey R , Loud Sara , McBurney Robert , Merkel Peter A , Sreih Antoine G , Young Kalen , Haynes Kevin 
Published: January 2019

Abstract

Objective
Patient-powered research networks (PPRNs) are a valuable source of patient-generated information. Diagnosis code-based algorithms developed by PPRNs can be used to query health plans’ claims data to identify patients for research opportunities. Our objective was to implement privacy-preserving record linkage processes between PPRN members’ and health plan enrollees’ data, compare linked and nonlinked members, and measure disease-specific confirmation rates for specific health conditions.

Materials and Methods
This descriptive study identified overlapping members from 4 PPRN registries and 14 health plans. Our methods for the anonymous linkage of overlapping members used secure Health Insurance Portability and Accountability Act–compliant, 1-way, cryptographic hash functions. Self-reported diagnoses by PPRN members were compared with claims-based computable phenotypes to calculate confirmation rates across varying durations of health plan coverage.

Results
Data for 21 616 PPRN members were hashed. Of these, 4487 (21%) members were linked, regardless of any expected overlap with the health plans. Linked members were more likely to be female and younger than nonlinked members were. Irrespective of duration of enrollment, the confirmation rates for the breast or ovarian cancer, rheumatoid or psoriatic arthritis or psoriasis, multiple sclerosis, or vasculitis PPRNs were 72%, 50%, 75%, and 67%, increasing to 91%, 67%, 93%, and 80%, respectively, for members with ≥5 years of continuous health plan enrollment.

Conclusions
This study demonstrated that PPRN membership and health plan data can be successfully linked using privacy-preserving record linkage methodology, and used to confirm self-reported diagnosis. Identifying and confirming self-reported diagnosis of members can expedite patient selection for research opportunities, shorten study recruitment timelines, and optimize costs.
Advances in population ecology and species interactions in mammals
Authors: Kelt Douglas A , Heske Edward J , Lambin Xavier , Oli Madan K , Orrock John L , Ozgul Arpat , Pauli Jonathan N , Prugh Laura R , Sollmann Rahel , Sommer Stefan 
Published: January 2019

AbstractThe study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.
Targeted Genomic Profiling of Acral Melanoma
Authors: Yeh Iwei , Jorgenson Eric , Shen Ling , Xu Mengshu , North Jeffrey P , Shain A Hunter , Reuss David , Wu Hong , Robinson William A , Olshen Adam , von Deimling Andreas , Kwok Pui-Yan , Bastian Boris C , Asgari Maryam M 
Published: January 2019

Abstract

Background
Acral melanoma is a rare type of melanoma that affects world populations irrespective of skin color and has worse survival than other cutaneous melanomas. It has relatively few single nucleotide mutations without the UV signature of cutaneous melanomas, but instead has a genetic landscape characterized by structural rearrangements and amplifications. BRAF mutations are less common than in other cutaneous melanomas, and knowledge about alternative therapeutic targets is incomplete.

Methods
To identify alternative therapeutic targets, we performed targeted deep-sequencing on 122 acral melanomas. We confirmed the loss of the tumor suppressors p16 and NF1 by immunohistochemistry in select cases.

Results
In addition to BRAF (21.3%), NRAS (27.9%), and KIT (11.5%) mutations, we identified a broad array of MAPK pathway activating alterations, including fusions of BRAF (2.5%), NTRK3 (2.5%), ALK (0.8%), and PRKCA (0.8%), which can be targeted by available inhibitors. Inactivation of NF1 occurred in 18 cases (14.8%). Inactivation of the NF1 cooperating factor SPRED1 occurred in eight cases (6.6%) as an alternative mechanism of disrupting the negative regulation of RAS. Amplifications recurrently affected narrow loci containing PAK1 and GAB2 (n = 27, 22.1%), CDK4 (n = 27, 22.1%), CCND1 (n = 24, 19.7%), EP300 (n = 20, 16.4%), YAP1 (n = 15, 12.3%), MDM2 (n = 13, 10.7%), and TERT (n = 13, 10.7%) providing additional and possibly complementary therapeutic targets. Acral melanomas with BRAFV600E mutations harbored fewer genomic amplifications and were more common in patients with European ancestry.

Conclusion
Our findings support a new, molecularly based subclassification of acral melanoma with potential therapeutic implications: BRAFV600E mutant acral melanomas with characteristics similar to nonacral melanomas that could benefit from BRAF inhibitor therapy, and non-BRAFV600E mutant acral melanomas. Acral melanomas without BRAFV600E mutations harbor a broad array of therapeutically relevant alterations. Expanded molecular profiling would increase the detection of potentially targetable alterations for this subtype of acral melanoma.
Percy Bysshe Shelley
Authors: Lacey Andrew 
Published: January 2019

Percy Bysshe Shelley (b. 1792–d. 1822) is now recognized as a major writer, chiefly a poet, of the Romantic period. His life was short, peripatetic, and frequently dogged by scandal. Treated badly in the reviews, he never knew great literary success in his lifetime. From privileged beginnings, Shelley quickly ran into trouble at Oxford: he was expelled in his second term, in 1811, for refusing to deny the authorship of the pamphlet The Necessity of Atheism. By the time of the private publication of his long “Philosophical Poem” Queen Mab (1813), Shelley had been married, increasingly unhappily, for nearly two years to Harriet Westbrook, who would later commit suicide in 1816. Having eloped with Mary Wollstonecraft Godwin in 1814, Shelley published his first major volume Alastor; or, The Spirit of Solitude: and Other Poems in early 1816, and the pair spent the summer of that year with Byron on the Continent, during which time Shelley wrote his famous lyrics “Hymn to Intellectual Beauty” and “Mont Blanc.” Shelley and Mary married in late 1816. Never secure in his finances, and feeling generally disillusioned with life in England, Shelley left for good in 1818, moving with Mary to Italy, where Byron, a firm influence, was residing. There, the Shelleys, Byron, and their circle lived as exiles, Shelley writing and publishing some of his finest poems, including Prometheus Unbound (1820), Epipsychidion, and Adonais (both 1821), all in spite of difficult personal circumstances: in his final years, Shelley endured grief (the deaths of his children Clara and William), anxiety (increasing strain in his relationship with Mary), and bouts of ill health (nephritis and ophthalmia). Before reaching the age of thirty, Shelley drowned in the Bay of Spezia, his boat, the Don Juan, having gone down in a storm. The twenty-four-year-old Mary, in the midst of a fresh bereavement, heroically took on the task of saving and copying Shelley’s manuscripts, publishing his Posthumous Poems in 1824; further (highly admirable, but flawed) editions of Shelley’s poetry and prose, also edited by Mary, followed (1839/40). Since his death, critical opinion on Shelley has varied wildly, and his reputation has been checkered. Famously, Matthew Arnold defined Shelley as “a beautiful and ineffectual angel, beating in the void his luminous wings in vain,” T. S. Eliot lamented that “the ideas of Shelley seem to me always to be ideas of adolescence,” and F. R. Leavis judged that he had “a weak grasp on the actual.” Since the 1950s in North America (later in Britain), Shelley’s status as an important writer, and his place on university syllabuses, has become more secure. This article will present, selectively, some of the most important sources on Shelley, concentrating primarily on post-1950s scholarship.
Preventing Controversial Catastrophes
Authors: Baker Steven D , Hollifield Burton , Osambela Emilio 
Published: January 2019

AbstractWe model, in a market-based democracy, different constituencies that disagree regarding the likelihood of economic disasters. Costly public policy initiatives to reduce or eliminate disasters are assessed relative to private alternatives presented by financial markets. Demand for such public policies falls as much as 40% with disagreement, and crowding out by private insurance drives most of the reduction. As support for disaster-reducing policy jumps in periods of disasters, costly policies may be adopted only after disasters occur. In some scenarios constituencies may even demand policies oriented at increasing disaster risk if these policies introduce speculative opportunities.Received September 25, 2017; Editorial decision September 3, 2018 by Editor: Thierry Foucault
Superficial and Deep Cutaneous Involvement by RAS-Associated Autoimmunne Leukoproliferative Disease (RALD Cutis): A Histologic Mimicker of Histiocytoid Sweet Syndrome
Authors: Tran Tien Anh N. , Grow William B. , Chang Chung-Che 
Published: January 2019

Abstract:
RAS-associated autoimmune leukoproliferative disease (RALD) is a recently described noninfectious and nonmalignant clinical syndrome characterized by autoimmune disorders, massive splenomegaly, modest lymphadenopathy, and monocytosis. On the molecular level, RALD is defined by somatic mutations of either NRAS or KRAS gene in a subset of hematopoietic cells. To date, there is a dearth of well-documented histopathologic description of cutaneous involvement by RALD in the literature. In the current case report, a 43-year-old female patient with a history of RALD presented with clinical pictures of sepsis and an erythematous rash in the left lower extremity. Histologic examination revealed a dense perivascular and interstitial infiltrate of immature myeloid cells admixed with scattered neutrophils involving the dermis and subcutaneous adipose tissue, imparting a panniculitis-like histologic pictures. There was a strong angiocentric propensity of the immature hematopoietic cells as well as extensive extravasation of red blood cells, even in the subcutaneous adipose tissue. Immunohistochemically, the immature hematopoietic cells were positive for CD43, CD4, and CD68, but negative for CD34, CD117, and myeloperoxidase. Overall, the histologic and cytologic findings were highly reminiscent of histiocytoid Sweet syndrome. Review of the English literature revealed cutaneous involvements by RALD only in patients with KRAS mutation compared with none of its NRAS counterparts. However, larger clinicopathologic studies on cutaneous involvement by RALD are warranted. The term “RALD cutis” with its histologic and molecular features is suggested to serve as a potential groundwork for future studies of this rare phenomenon.