bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yellowstone Hot Springs are Organic Chemodiversity Hot Spots
Authors: Gonsior Michael , Hertkorn Norbert , Hinman Nancy , Dvorski Sabine E.-M. , Harir Mourad , Cooper William J. , Schmitt-Kopplin Philippe 
Published: September 2018

AbstractYellowstone National Park hydrothermal springs were investigated according to their organic geochemistry with a special focus on the Yellowstone hot spring dissolved organic matter (YDOM) that was solid-phase extracted. Here we show that YDOM has a unique chemodiversity that has not yet been observed anywhere else in aquatic surface environments and that Yellowstone hot springs are organic chemodiversity hot spots. Four main geochemically classified hot spring types (alkaline-chloride, mixed alkaline-chloride, acid-chloride-sulfate and travertine-precipitating) exhibited distinct organic molecular signatures that correlated remarkably well with the known inorganic geochemistry and manifested themselves in excitation emission matrix fluorescence, nuclear magnetic resonance, and ultrahigh resolution mass spectra. YDOM contained thousands of molecular formulas unique to Yellowstone of which 80% contained sulfur, even in low hydrogen sulfide containing alkaline-chloride springs. This unique YDOM reflects the extreme organic geochemistry present in the hydrothermal features of Yellowstone National Park.
The digital transformation of medicine can revitalize the patient-clinician relationship
Authors: Warraich Haider J. , Califf Robert M. , Krumholz Harlan M. 
Published: September 2018

AbstractHealth professionals within the medical community feel that the principles of humanism in medicine have not been a point of emphasis for information and computer technology in healthcare. There is concern that the electronic health record is eroding the patient-clinician relationship and distancing clinicians from their patients. New analytic technologies, on the contrary, by taking over repetitive and mundane tasks, can provide an avenue to make medical care more patient-centered by freeing clinicians’ time, and the time of the whole clinical care team, to engage with patients. Technology such as advanced speech recognition that optimizes clinicians’ workflow could revitalize the patient-clinician relationship and perhaps also improve clinician well-being. Digital phenotyping can gain invaluable additional data from patients using technology that is already used for personal reasons by the majority of patients. The digital transformation of healthcare has the potential to make healthcare more humane and personalized, however, several important steps are needed to avoid the pitfalls that have come with prior iterations of information technology in medicine such as a heightened emphasis on data security and transparency. Both patients and clinicians should be involved from the early stages of development of medical technologies to ensure that they are person-centric. Technologists and engineers developing healthcare technologies should have experiences with the delivery of healthcare and the lives of patients and clinicians. These steps are necessary to develop a common commitment to the design concept that technology and humane care are not mutually exclusive, and in fact, can be symbiotic.
Interfacial energy as a selection mechanism for minimizing gradient Young measures in a one-dimensional model problem
Authors: Della Porta Francesco 
Published: September 2018

Energy functionals describing phase transitions in crystalline solids are often non-quasiconvex and minimizers might therefore not exist. On the other hand, there might be infinitely many gradient Young measures, modelling microstructures, generated by minimizing sequences, and it is an open problem how to select the physical ones.In this work we consider the problem of selecting minimizing sequences for a one-dimensional three-well problemε. We introduce a regularizationεεofεwith anε-small penalization of the second derivatives, and we obtain asε↓ 0 its Γ-limit and, under some further assumptions, the Γ-limit of a suitably rescaled version ofεε. The latter selects a unique minimizing gradient Young measure of the former, which is supported just in two wells and not in three. We then show that some assumptions are necessary to derive the Γ-limit of the rescaled functional, but not to prove that minimizers ofεεgenerate, asε↓ 0, Young measures supported just in two wells and not in three.
Optimizing the Multi-Objective Deployment Problem of Mlat System
Authors: Fadil Rabie , Abou El Majd Badr , El Ghazi Hassan , Rahil Hicham 
Published: September 2018

Multilateration (MLAT) systems are powerful means for air traffic surveillance. These systems aim to extract, and display to air traffic controllers identification of aircrafts or vehicles equipped with a transponder. They provide an accurate and real-time data without human intervention using a number of ground receiving stations, placed in some strategic locations around the coverage area, and they are connected with a Central Processing Subsystem (CPS) to compute the target (i.e., aircraft or vehicle) position. The MLAT performance strongly depends on system layout design which consists on deploying the minimum number of stations, in order to obtain the requested system coverage and performance, meeting all the regulatory standards with a minimum cost. In general, choosing the number of stations and their locations to cope with all the requirements is not an obvious task and the system designer has to make several attempts, by trial and error, before obtaining a satisfactory spatial distribution of the stations.
In this work we propose a new approach to solve the deployment of Mlat stations problem by focusing on the number of deployed stations and the coverage as the main objectives to optimize. The Non-dominated Sorting Genetic Algorithm II(NSGA-II) was used in order to minimize the total number of stations required to identify all targets in a given area, with the aim to minimize the deployment cost, accelerating processes, and achieve high availability and reliability. The proposed approach is more efficient and converge rapidly which makes it ideal for our research involving optimal deployment of Mlat station.
Early Failure in Medial Unicondylar Arthroplasty: Radiographic Analysis on the Importance of Joint Line Restoration
Authors: Lo Presti Mirco , Raspugli Giovanni Francesco , Reale Davide , Iacono Francesco , Zaffagnini Stefano , Filardo Giuseppe , Marcacci Maurilio 
Published: September 2018

AbstractSurvivorship of unicondylar knee arthroplasty (UKA) remains a drawback, especially compared with the outcome of total knee arthroplasty. This could be improved by identifying and correcting failure mechanisms. To this purpose, this study aimed at exploring failure modalities of UKA, with particular focus on the role of joint line (JL) position and alignment as variable to be optimized for a successful outcome. This study explored modes of failure in 266 medial UKAs. Radiological comparison was performed between 24 failures and 24 matched controls, to determine the importance of UKA positioning in terms of femorotibial angle (FTA), tibial plateau angle, and posterior tibial slope (PTS). Radiographic comparative analysis showed statistically significant differences in the failure group compared with the control group in terms of variation in FTA (p = 0.0222), PTS (p = 0.0025), and JL height (p = 0.0022). Variations not only in FTA but also PTS and JL height were correlated with failures observed in this series. Thus, based on the results of this study, it emerges that JL position should be carefully controlled in all planes while implanting a UKA. This is a Level III, case–control study.
Outcomes of Anterior Cruciate Ligament Reconstruction in Females Using Patellar–Tendon–Bone versus Hamstring Autografts: A Systematic Review and Meta-Analysis
Authors: Tan Si Heng Sharon , Lau Bernard Puang Huh , Krishna Lingaraj 
Published: September 2018

AbstractThe current review aims to compare the outcomes of anterior cruciate ligament (ACL) reconstruction in the female population after patellar–tendon–bone and hamstring grafts. The review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. All original randomized controlled trials and prospective cohort studies that compared clinical outcomes after female ACL reconstruction using hamstring versus patellar–tendon–bone grafts were included. All clinical outcomes reported by three or more studies were included. Fifteen publications, with 948 female patients, were included. Most outcomes were reported to have no significant graft differences by all studies that reported the outcome. These included all the outcomes for objective knee scores (International Knee Documentation Committee [IKDC] objective knee score), neuromuscular testing (quadriceps strength, hamstring strength, and single hop test), graft rupture or failure, and subjective knee scores (Lysholm score and IKDC subjective knee score). The pivot shift test, flexion deficit, and presence of crepitus were also reported to have no significant graft differences by all studies. Some studies reported a significant difference in anteroposterior laxity (Lachman's test and instrumented laxity), range of motion deficits (extension deficit), and sports and activity level (Tegner score). However, these statistically significant differences were noted to be clinically insignificant due to the normal population variation or standard error of measurement of these tools of evaluation. Patients reconstructed with patellar-tendon–bone grafts have a higher risk of kneeling pain. There was no significant difference in the incidence of crepitus. Most of the outcomes following female ACL reconstructions showed no clinically and statistically significant difference when either patellar–tendon–bone or hamstring autograft was used. These included outcomes for anteroposterior laxity, objective knee scores, neuromuscular testing, graft rupture or failure, subjective knee scores, sports and activity level, and crepitus. This a level II study.
On self-avoiding polygons and walks: The snake method via pattern fluctuation
Authors: Hammond Alan 
Published: September 2018

For

d
≥
2

d \geq 2

and

n
∈

N

n \in \mathbb {N}

, let

W

n

\mathsf {W}_n

denote the uniform law on self-avoiding walks of length

n
n

beginning at the origin in the nearest-neighbour integer lattice

Z

d

\mathbb {Z}^d

, and write

Γ
\Gamma

for a

W

n

\mathsf {W}_n

-distributed walk. We show that in the closing probability

W

n

(

|
|

Γ
n

|
|
=
1

)

\mathsf {W}_n \big ( \vert \vert \Gamma _n \vert \vert = 1 \big )

that

Γ
\Gamma

’s endpoint neighbours the origin and is at most

n

−
1

/

2
+
o
(
1
)

n^{-1/2 + o(1)}

in any dimension

d
≥
2

d \geq 2

. The method of proof is a reworking of that in [Ann. Probab. 44 (2016), pp. 955–983], which found a closing probability upper bound of

n

−
1

/

4
+
o
(
1
)

n^{-1/4 + o(1)}

. A key element of the proof is made explicit and called the snake method. It is applied to prove the

n

−
1

/

2
+
o
(
1
)

n^{-1/2 + o(1)}

upper bound by means of a technique of Gaussian pattern fluctuation.
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization
Authors: Luo Yuan , Mao Chengsheng , Yang Yiben , Wang Fei , Ahmad Faraz S , Arnett Donna , Irvin Marguerite R , Shah Sanjiv J 
Published: September 2018

Abstract

Motivation
Hypertension is a heterogeneous syndrome in need of improved subtyping using phenotypic and genetic measurements with the goal of identifying subtypes of patients who share similar pathophysiologic mechanisms and may respond more uniformly to targeted treatments. Existing machine learning approaches often face challenges in integrating phenotype and genotype information and presenting to clinicians an interpretable model. We aim to provide informed patient stratification based on phenotype and genotype features.

Results
In this article, we present a hybrid non-negative matrix factorization (HNMF) method to integrate phenotype and genotype information for patient stratification. HNMF simultaneously approximates the phenotypic and genetic feature matrices using different appropriate loss functions, and generates patient subtypes, phenotypic groups and genetic groups. Unlike previous methods, HNMF approximates phenotypic matrix under Frobenius loss, and genetic matrix under Kullback-Leibler (KL) loss. We propose an alternating projected gradient method to solve the approximation problem. Simulation shows HNMF converges fast and accurately to the true factor matrices. On a real-world clinical dataset, we used the patient factor matrix as features and examined the association of these features with indices of cardiac mechanics. We compared HNMF with six different models using phenotype or genotype features alone, with or without NMF, or using joint NMF with only one type of loss We also compared HNMF with 3 recently published methods for integrative clustering analysis, including iClusterBayes, Bayesian joint analysis and JIVE. HNMF significantly outperforms all comparison models. HNMF also reveals intuitive phenotype–genotype interactions that characterize cardiac abnormalities.

Availability and implementation
Our code is publicly available on github at https://github.com/yuanluo/hnmf.

Supplementary information
Supplementary data are available at Bioinformatics online.
FA01.03: USE OF ‘NON-TUBE NO FASTING’ ERAS PROTOCOL IN PATIENTS AFTER MIE WITH LI’S ANASTOMOSIS: OUTCOMES IN THE FIRST 113 PATIENTS PERFORMED BY A SURGEON AFTER TRAINING COURSE
Authors: Zhang Ruixiang , Li Yin , Liu Shilei , Liu Xianben , Sun Haibo , Wang Zongfei , Zheng Yan , Chen Xiankai , Liu Qi , Zhu Zhengshuai , Xu Lei 
Published: September 2018

Abstract

Background
Use of enhanced recovery after surgery(ERAS) protocol in the patients after esophagectomy is reported to be feasible and safe in recent studies. And in Prof. Yin Li's research, patients after minimally invasive esophagectomy(MIE) with Li's anastomosis took oral feeding on the 1st day after operation (POD1). However, all the esophagectomy-procedures were proceeded by experienced experts. There was no report regarding whether ERAS protocol after MIE with Li's anastomosis could be safely proceeded by a young surgeon after training course. The aim of this study was to evaluate the feasibility and safety of ‘Non-Tube No Fasting’ ERAS Protocol in patients after MIE with Li's Anastomosis proceeded by a surgeon after the training course.

Methods
We retrospectively reviewed the clinical data of patients who underwent MIE for cancer from December 2015 to September 2017 by a new surgical team finished MIE training course in our department. During the study period, the new team performed Mckeown MIE with Li's anastomosis for 127 esophageal cancer patients. We analyzed the data of 113 patients who followed the protocol of ‘Non-tube No Fasting’ ERAS. The primary end-points were the incidence of anastomotic fistula, the injury of recurrent laryngeal nerve, pneumonia, and postoperative length of hospital-stay.

Results
All the 113 patients began oral feeding on POD1. Two patients exited the ERAS protocol on account of bucking caused by recurrent laryngeal nerve injury on POD3. The incidence of anastomotic fistula, recurrent laryngeal nerve injury and pneumonia were 3.5% (4/113), 12.4%(14/113) and 18.5%(21/113). The average length of postoperative hospital-stay was 8.6 ± 6.9 days. Both of the in-hospital mortality and 30-day mortality were 0.

Conclusion
Our date indicated that it was feasible and safe for a selected surgeon after ‘Non-tube no fasting’ ERAS and MIE training courses to proceed the protocol. Of course, more clinical researches are needed to confirm this result.

Disclosure
All authors have declared no conflicts of interest.
Advancing Research on Psychosocial Stress and Aging with the Health and Retirement Study: Looking Back to Launch the Field Forward
Authors: Crosswell Alexandra D , Suresh Madhuvanthi , Puterman Eli , Gruenewald Tara L , Lee Jinkook , Epel Elissa S 
Published: September 2018

Abstract

Objectives
The Health and Retirement Study (HRS) was designed as an interdisciplinary study with a strong focus on health, retirement, and socioeconomic environment, to study their dynamic relationships over time in a sample of mid-life adults. The study includes validated self-report measures and individual items that capture the experiences of stressful events (stressor exposures) and subjective assessments of stress (perceived stress) within specific life domains.

Methods
This article reviews and catalogs the peer-reviewed publications that have used the HRS to examine associations between psychosocial stress measures and psychological, physical health, and economic outcomes.

Results
We describe the research to date using HRS measures of the following stress types: traumatic and life events, childhood adversity, caregiving and other chronic stressors, discrimination, social strain and loneliness, work stress, and neighborhood disorder. We highlight how to take further advantage of the longitudinal study to test complex biopsychosocial models of healthy aging.

Discussion
The HRS provides one of the most comprehensive assessments of psychosocial stress in existing population-based studies and offers the potential for a deeper understanding of how psychosocial factors are related to healthy aging trajectories. The next generation of research examining stress and trajectories of aging in the HRS should test complex longitudinal and mediational relationships, include contextual factors in analyses, and include more collaboration between psychologists and population health researchers.
The 22q11 low copy repeats are characterized by unprecedented size and structure variability
Authors: Demaerel Wolfram , Mostovoy Yulia , Yilmaz Feyza , Vervoort Lisanne , Pastor Steven , Hestand Matthew S , Swillen Ann , Vergaelen Elfi , Geiger Elizabeth A. , Coughlin Curtis R. , Chow Stephen K. , McDonald-McGinn Donna , Morrow Bernice , Kwok Pui-Yan , Xiao Ming , Emanuel Beverly S. , Shaikh Tamim H. , Vermeesch Joris R 
Published: September 2018

Abstract:Low copy repeats (LCRs) are recognized as a significant source of genomic instability, driving genome variability and evolution. The chromosome 22 LCRs (LCR22s) are amongst the most complex regions in the genome and their structure remains unresolved. These LCR22s mediate non-allelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS), causing the most frequent genomic disorder. Using fiber FISH optical mapping, we have de novo assembled the LCR22s in 33 cell lines. We observed a high level of variation in LCR22 structures, including 26 different haplotypes of LCR22A with alleles ranging from 250 Kb to over 2,000 Kb. An additional four haplotypes were detected using Bionano mapping. Further, Bionano maps generated from 154 individuals from different populations suggested significantly different LCR22 haplotype frequencies between populations. Furthermore, haplotype analysis in nine 22q11DS patients resulted in the localization of the NAHR site to a 160 Kb paralog between LCR22A and –D in seven patients and to a 31 Kb region in two individuals with a rearrangement between LCR22A and –B.. This 31 Kb region contains a palindromic AT-rich repeat known to be a driver of chromosomal rearrangements. Our study highlights an unprecedented level of polymorphism in the structure of LCR22s, which are likely still evolving. We present the most comprehensive map of LCR22 variation to date, paving the way towards investigating the role of LCR variation as a driver of 22q11 rearrangements and the phenotypic variability in 22q11DS patients as well as in the general population.
Modular mathematical analysis of the control of flagellar Ca2+-spike trains produced by CatSper and CaVchannels in sea urchin sperm
Authors: Priego-Espinosa D.A. , Darszon A. , Guerrero A. , González-Cota A.L. , Nishigaki T. , Martinez-Mekler G. , Carneiro J. 
Published: September 2018

AbstractIntracellular calcium ([Ca2+]i) is a basic, versatile and ubiquitous cellular signal controlling a wide variety of biological processes. A remarkable example is the steering of sea urchin spermatozoa towards the conspecific egg by a spatially and temporally orchestrated series of cytosolic [Ca2+]ispikes. Although this process has been an experimental paradigm for reproduction and sperm chemotaxis studies, the composition and regulation of the signalling network underlying the cytosolic calcium fluctuations are hitherto not fully understood. Here, we used a differential equations model of the signalling network to assess which set of channels can explain the characteristic envelop and temporal organisation of the [Ca2+]i-spike trains. The signalling network comprises an initial membrane hyperpolarisation/repolarisation produced by an upstream module triggered by the egg-released chemoattractant peptide, via receptor activation, cGMP synthesis and decay. Followed by downstream modules leading to pHi, voltage and [Ca2+]ifluctuations. The upstream module outputs were fitted to kinetic data on cGMP activity and early membrane potential changes measured in bulk cell populations. Two candidate modules featuring voltage-dependent Ca2+-channels link these outputs to the downstream dynamics and can independently explain the typical decaying envelop and the progressive spacing of the spikes. In the first module, [Ca2+]i-spike trains require the concerted action of a classical CaV-like channel and a potassium channel, BK (Slo1), whereas the second module relies on pHi-dependent, [Ca2+]i-inactivated CatSper dynamics alone. The model predicts that these two modules interfere with each other and produce unreasonable dynamics when present at similar proportions, which suggests that one may predominate over the otherin vivo. To assess these alternatives, several quantitative predictions were derived from each module and confronted to experimental observations. We show that the [Ca2+]Idynamics observed experimentally after sustained alkalinisation can be reproduced by a model featuring the CatSper module but not by one including the pH-independent CaVand BK module. We conclude in favour of the module containing CatSper.
A molecular model of the surface-assisted protein aggregation process
Authors: Pan Y.G. , Banerjee S. , Zagorski K. , Shlyakhtenko L.S. , Kolomeisky A.B. , Lyubchenko Y. L. 
Published: September 2018

AbstractThe importance of cell surfaces in the self-assembly of proteins is widely accepted. One biologically significant event is the assembly of amyloidogenic proteins into aggregates, which leads to neurodegenerative disorders like Alzheimer’s and Parkinson’s. The interaction of amyloidogenic proteins with cellular membranes appears to dramatically facilitate the aggregation process. Recent findings indicate that, in the presence of surfaces, aggregation occurs at physiologically low concentrations, suggesting interaction with surfaces plays a critical role in the disease-prone aggregation process. However, the molecular mechanisms behind on-surface aggregation remain unclear. Here we provide a theoretical model that offers a molecular explanation. According to this model, monomers transiently immobilized to surfaces increase the local monomer protein concentration and thus work as nuclei to dramatically accelerate the entire aggregation process. This theory was verified by experimental studies, using mica surfaces, to examine the aggregation kinetics of amyloidogenic-synuclein protein (α-Syn) and non-amyloidogenic cytosine deaminase APOBEC3G (A3G).