bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of Sediment Transport Discharges of Citarum River, West Java In Laboratory
Authors: Pranoto Wati A. , Subari dan Marvin 
Published: October 2019

Abstract
Citarum River is one of the longest and largest rivers in Indonesia located in West Java with a length of 300 km. The Citarum River carries the sediment in the water stream from the erosion. This study focused on bed load sediment transport. The study of sediment transport is still a few, but some experts have proposed the formula to calculate the amount of sediment transport such as Einstein, Shields, and Schoklitsch. A research in Hydraulics Laboratory and Soil Mechanics Laboratory is conducted to examine the bed load transport from the Citarum River. The purpose of this study is to analyze and compare the result of discharge obtained from the laboratory with the Einstein, Shields, and Schoklitsch approach.
Distribution fitting on rainfall data in Jakarta
Authors: Kurniawan V 
Published: October 2019

Abstract
The estimation of design flood or rainfall for various return periods is not easy due to the difficulty in finding the fitting distribution for the corresponding data. This study focuses on selecting the best distribution in representing rainfall data from Kemayoran rain gauge (Jakarta, Indonesia) for the last 20 years. The objective is to probe the most fitting distribution for Jakarta. This study applies goodness of fit tests to Kemayoran rainfall data. The result is quite unexpected as the best fitting distributions are not commonly used in flood frequency analysis (FFA) subject and most of them are distributions with three parameters. The referred distributions in Indonesia national standard for flood estimation (SNI 2415:2016) produce mixed results. The classic distributions in FFA e.g. Lognormal 3P and Log-Pearson 3 show good compatibility to the corresponding data while the less prevalent distributions such as Lognormal and Normal are not as compatible.
Sediment Characteristics of Bed Load Transport in Downstream of Progo River, Indonesia
Authors: Ikhsan J , Wardhana C , Widiyarto D K 
Published: October 2019

Abstract
Progo River is one of the rivers that has a sediment supply from volcanic and non-volcanic areas. Sediment transport, especially the bed load transport, it is very influential on the phenomenon of river degradation and aggradation. Therefore, a study to determine the characteristics of bed load transport is needed and important. The research was carried out in the downstream part of Progo River. Sampling locations were taking in four locations, namely Ancol Bridge, Kebon Agung II Bridge, Kebon Agung I Bridge and Bantar Bridge. The bed load transport measurement tool was used Helley Smith (WMO, 1980) equipment. Every river cross section is taken three times. The results showed that the sediment type of bed load transports is silty sand, with specific gravity values of 2.67 to 2.70. The average diameter values (D50) of the bed load transports vary greatly from 0.129 mm to 0.454 mm. The values of bed load transports vary greatly and are influenced by the values of the discharges. The correlation between bed load transport and discharge is linear, with R values are 0.85 to 0.99.
Tensile and flexural behaviour of a graphene/epoxy composite: experiments and simulation
Authors: Manta Asimina , Gresil Matthieu , Soutis Constantinos 
Published: October 2019

Abstract
The tensile and flexural behaviour of a graphene nanoplatelet (GnP) reinforced polymer, Grade M25 GnP / Araldite LY564 is experimentally investigated. This is followed by a multi-scale finite element model to simulate the tensile response as the most critical loading case. The approach is based on the multi-scale method and consists of a unit cell and a representative volume element (RVE). At the unit cell level, the material nanocharacteristics (filler geometry, phase mechanical properties, interfacial properties) are used to calculate the local tensile response. The material architecture is simulated at the RVE level by distributing the locally obtained unit cell mechanical properties, using periodic boundary conditions. A statistical sample was studied and the average mechanical characteristics were compared to the macroscopic measured stress–strain data. Finally, the simulation methodology was validated by comparisons between the effective experimental and numerical results.
A dimension-free Hermite–Hadamard inequality via gradient estimates for the torsion function
Authors: Lu Jianfeng , Steinerberger Stefan 
Published: October 2019

Let

Ω
⊂

R

n

\Omega \subset \mathbb {R}^n

be a convex domain, and let

f
:
Ω
→

R

f:\Omega \rightarrow \mathbb {R}

be a subharmonic function,

Δ
f
≥
0

\Delta f \geq 0

, which satisfies

f
≥
0

f \geq 0

on the boundary

∂
Ω

\partial \Omega

. Then

∫

Ω

f

d
x

≤

|

Ω

|

1
n

∫

∂
Ω

f

d
σ

.

\begin{equation*} \int _{\Omega }{f ~dx} \leq |\Omega |^{\frac {1}{n}} \int _{\partial \Omega }{f ~d\sigma }. \end{equation*}

Our proof is based on a new gradient estimate for the torsion function,

Δ
u
=
−
1

\Delta u = -1

with Dirichlet boundary conditions, which is of independent interest.
Mixed Bohr radius in several variables
Authors: Galicer Daniel , Mansilla Martín , Muro Santiago 
Published: October 2019

Let

K
(

B

ℓ
p
n

,

B

ℓ
q
n

)

K(B_{\ell _p^n},B_{\ell _q^n})

be the

n
n

-dimensional

(
p
,
q
)

(p,q)

-Bohr radius for holomorphic functions on

C

n

\mathbb {C}^n

. That is,

K
(

B

ℓ
p
n

,

B

ℓ
q
n

)

K(B_{\ell _p^n},B_{\ell _q^n})

denotes the greatest number

r
≥
0

r\geq 0

such that for every entire function

f
(
z
)
=

∑

α

a

α

z

α

f(z)=\sum _{\alpha } a_{\alpha } z^{\alpha }

in

n
n

-complex variables, we have the following (mixed) Bohr-type inequality:

sup

z
∈
r
⋅

B

ℓ
q
n

∑

α

|

a

α

z

α

|
≤

sup

z
∈

B

ℓ
p
n

|
f
(
z
)
|
,

\begin{equation*} \sup _{z \in r \cdot B_{\ell _q^n}} \sum _{\alpha } \vert a_{\alpha } z^{\alpha } \vert \leq \sup _{z \in B_{\ell _p^n}} \vert f(z) \vert , \end{equation*}

where

B

ℓ
r
n

B_{\ell _r^n}

denotes the closed unit ball of the

n
n

-dimensional sequence space

ℓ
r
n

\ell _r^n

.

For every

1
≤
p
,
q
≤
∞

1 \leq p, q \leq \infty

, we exhibit the exact asymptotic growth of the

(
p
,
q
)

(p,q)

-Bohr radius as

n
n

(the number of variables) goes to infinity.
Risk factors for development of aminoglycoside resistance among gram-negative rods
Authors: Richter Stefan E , Miller Loren , Needleman Jack , Uslan Daniel Z , Bell Douglas , Watson Karol , Humphries Romney , McKinnell James A 
Published: October 2019

Abstract

Purpose
Development of scoring systems to predict the risk of aminoglycoside resistance and to guide therapy is described.

Methods
Infections due to aminoglycoside-resistant gram-negative rods (AR-GNRs) are increasingly common and associated with adverse outcomes; selection of effective initial antibiotic therapy is necessary to reduce adverse consequences and shorten length of stay. To determine risk factors for AR-GNR recovery from culture, cases of GNR infection among patients admitted to 2 institutions in a major academic hospital system during the period 2011–2016 were retrospectively analyzed. Gentamicin and tobramycin resistance (GTR-GNR) and amikacin resistance (AmR-GNR) patterns were analyzed separately. A total of 26,154 GNR isolates from 12,516 patients were analyzed, 6,699 of which were GTR, and 2,467 of which were AmR.

Results
In multivariate analysis, risk factors for GTR-GNR were presence of weight loss, admission from another medical or long-term care facility, a hemoglobin level of &lt;11 g/dL, receipt of any carbapenem in the prior 30 days, and receipt of any fluoroquinolone in the prior 30 days (C statistic, 0.63). Risk factors for AmR-GNR were diagnosis of cystic fibrosis, male gender, admission from another medical or long-term care facility, ventilation at any point prior to culture during the index hospitalization, receipt of any carbapenem in the prior 30 days, and receipt of any anti-MRSA agent in the prior 30 days (C statistic, 0.74). Multinomial and ordinal models demonstrated that the risk factors for the 2 resistance patterns differed significantly.

Conclusion
A scoring system derived from the developed risk prediction models can be applied by providers to guide empirical antimicrobial therapy for treatment of GNR infections.
The Leaky Pipeline of Women in Plastic Surgery: Embracing Diversity to Close the Gender Disparity Gap
Authors: Moak Teri N , Cress Phaedra E , Tenenbaum Marissa , Casas Laurie A 
Published: October 2019

Abstract
The Balance for Better campaign theme of the 2019 International Women’s Day prompted a closer look at diversity within the plastic surgery specialty. Gender balance in the United States has improved through many organizational efforts and enactment of laws. Unfortunately, despite these endeavors, statistics show that men still enjoy greater financial and career success. Within the field of medicine, a similar trend has been observed. Although women constitute 50% of medical school graduates, the majority still enter fields outside of surgical subspecialties. In comparison to other surgical subspecialties, women are most represented in plastic surgery. Unfortunately, significant gender discrepancies remain in postgraduate practice including academic practice rank, societal board membership, invited speaker opportunities, and compensation, to name a few. The “leaky pipeline” of women describes the precipitous decline in the numbers of women at each step up the professional ladder. We explore the multifaceted nature of this phenomenon and highlight factors that contribute to limiting female growth within the plastic surgery profession. We also emphasize the continued growth of female plastic surgeon presence in all sectors despite these existing obstacles. We submit that continued leadership, mentorship, and sponsorship provided by both male and female physicians in the field will facilitate future leadership, advance gender parity, and cultivate a sense of belonging within the plastic surgery community, allowing brilliant minds to flourish and the profession to thrive.
GenCLiP 3: mining human genes’ functions and regulatory networks from PubMed based on co-occurrences and natural language processing
Authors: Wang Jia-Hong , Zhao Ling-Feng , Wang Hua-Feng , Wen Yue-Ting , Jiang Kui-Kui , Mao Xiang-Ming , Zhou Zi-Ying , Yao Kai-Tai , Geng Qing-Shan , Guo Dan , Huang Zhong-Xi 
Published: October 2019

Abstract

Summary
We present a web server, GenCLiP 3, which is an updated version of GenCLiP 2.0 to enhance analysis of human gene functions and regulatory networks, with the following improvements: (i) accurate recognition of molecular interactions with polarity and directionality from the entire PubMed database; (ii) support for Boolean search to customize multiple-term search and to quickly retrieve function-related genes; (iii) strengthened association between gene and keyword by a new scoring method; and (iv) daily updates following literature release at PubMed FTP.

Availability and implementation
The server is freely available for academic use at: http://ci.smu.edu.cn/genclip3/.

Supplementary information
Supplementary data are available at Bioinformatics online.
PRODIGY: personalized prioritization of driver genes
Authors: Dinstag Gal , Shamir Ron 
Published: October 2019

Abstract

Motivation
Evolution of cancer is driven by few somatic mutations that disrupt cellular processes, causing abnormal proliferation and tumor development, whereas most somatic mutations have no impact on progression. Distinguishing those mutated genes that drive tumorigenesis in a patient is a primary goal in cancer therapy: Knowledge of these genes and the pathways on which they operate can illuminate disease mechanisms and indicate potential therapies and drug targets. Current research focuses mainly on cohort-level driver gene identification but patient-specific driver gene identification remains a challenge.

Methods
We developed a new algorithm for patient-specific ranking of driver genes. The algorithm, called PRODIGY, analyzes the expression and mutation profiles of the patient along with data on known pathways and protein–protein interactions. Prodigy quantifies the impact of each mutated gene on every deregulated pathway using the prize-collecting Steiner tree model. Mutated genes are ranked by their aggregated impact on all deregulated pathways.

Results
In testing on five TCGA cancer cohorts spanning &gt;2500 patients and comparison to validated driver genes, Prodigy outperformed extant methods and ranking based on network centrality measures. Our results pinpoint the pleiotropic effect of driver genes and show that Prodigy is capable of identifying even very rare drivers. Hence, Prodigy takes a step further toward personalized medicine and treatment.

Availability and implementation
The Prodigy R package is available at: https://github.com/Shamir-Lab/PRODIGY.

Supplementary information
Supplementary data are available at Bioinformatics online.
Transmural Histological Scoring Systems in Crohn’s Disease: A Systematic Review With Assessment of Methodological Quality and Operating Properties
Authors: Tavares de Sousa Helena , Estevinho Maria Manuela , Peyrin-Biroulet Laurent , Danese Silvio , Dias Cláudia Camila , Carneiro Fátima , Magro Fernando 
Published: October 2019

Abstract

Background
The relative proportion of inflammation and fibrosis in a stricture is highly relevant in defining the clinical approach for Crohn’s disease [CD] patients. Whereas transmural inflammation in CD can be accurately estimated by cross-sectional imaging, evaluating the extent and severity of fibrosis still requires surgical pathology of intestinal resection specimens. This study systematically reviewed all existing transmural histopathological scoring systems developed for the assessment of inflammation and/or fibrosis in CD.

Methods
A systematic review of histopathological scoring systems for the assessment of transmural inflammation and/or fibrosis in CD, focusing on originally developed scoring systems. Risk of bias, methodological quality, and operating or psychometric properties [validity, reliability, responsiveness, and feasibility] of each histological scoring system were analysed.

Results
A total of 29 original scoring systems were included in this review. Three scoring systems were highlighted as the most widely reproduced, one aimed at assessing inflammation only and two aimed at assessing inflammation and fibrosis. These scores were more widely reproduced probably due to their ease of application in clinical studies. Two highly comprehensive scores were identified, showing good operating properties and high methodological quality, as well as the lowest risk of bias; these should, therefore, be further validated in clinical research studies.

Conclusions
This study reviewed all existing transmural histopathological scoring systems for the assessment of inflammation and/or fibrosis in CD and identified the most reliable and accurate scores for clinical research and clinical practice settings.
The use of serial cardiac 18F-fluorodeoxyglucose– positron emission tomography imaging to diagnose, monitor, and tailor treatment of cardiac sarcoidosis patients with arrhythmias: a case series and review
Authors: Kersey Cooper B , Flaherty Kathleen R , Goldenthal Isaac L , Bokhari Sabahat , Biviano Angelo B 
Published: October 2019

Abstract

Background
Clinically evident cardiac involvement has been documented in 5% of sarcoidosis patients, primarily manifesting as heart block, ventricular arrhythmias, and heart failure. Heart Rhythm Society consensus guidelines recommend advanced cardiac imaging with fluorodeoxyglucose–positron emission tomography (FDG-PET) scan for diagnosis of cardiac sarcoidosis, given endomyocardial biopsy’s low sensitivity.

Case summary
We describe four patients with cardiac sarcoidosis diagnosed with FDG-PET scan performed using a standardized imaging protocol for cardiac sarcoidosis. Serial FDG-PET scans were performed to monitor disease progression and response to therapy. Patients 1 and 2 presented with heart block, Patient 3 with heart failure and ventricular tachycardia (VT), and Patient 4 with VT. Patient 1 showed an initial decrease in standard uptake value (SUV) on immunosuppression, followed by an increase in SUV, necessitating steroid therapy. Patient 2’s SUV decreased on immunosuppression. Patient 3 required 3.5 years of immunosuppression for the SUV to decrease to inactive disease levels, with SUV increasing and decreasing at different times during treatment, and subsequently developed VT. For Patient 4, areas of inflammation on the initial scan matched low voltage areas on the patient’s EP study, confirming the arrhythmia’s pathophysiological basis.

Discussion
Cardiac sarcoidosis progression and response to therapy are heterogeneous. Serial FDG-PET scans are useful to diagnose disease, tailor therapy, and monitor the clinical course of disease, allowing treatment decisions to be based on the quantitative level of inflammation seen on FDG-PET.
Treatment outcome with orthodontic aligners and fixed appliances: a systematic review with meta-analyses
Authors: Papageorgiou Spyridon N , Koletsi Despina , Iliadi Anna , Peltomaki Timo , Eliades Theodore 
Published: October 2019

SummaryBackgroundThe use of orthodontic aligners to treat a variety of malocclusions has seen considerable increase in the last years, yet evidence about their efficacy and adverse effects relative to conventional fixed orthodontic appliances remains unclear.ObjectiveThis systematic review assesses the efficacy of aligners and fixed appliances for comprehensive orthodontic treatment.Search methodsEight databases were searched without limitations in April 2019.Selection criteriaRandomized or matched non-randomized studies.Data collection and analysisStudy selection, data extraction, and risk of bias assessment was done independently in triplicate. Random-effects meta-analyses of mean differences (MDs) or relative risks (RRs) with their 95% confidence intervals (CIs) were conducted, followed by sensitivity analyses, and the GRADE analysis of the evidence quality.ResultsA total of 11 studies (4 randomized/7 non-randomized) were included comparing aligners with braces (887 patients; mean age 28.0 years; 33% male). Moderate quality evidence indicated that treatment with orthodontic aligners is associated with worse occlusal outcome with the American Board of Orthodontics Objective Grading System (3 studies; MD = 9.9; 95% CI = 3.6–16.2) and more patients with unacceptable results (3 studies; RR = 1.6; 95% CI = 1.2–2.0). No significant differences were seen for treatment duration. The main limitations of existing evidence pertained to risk of bias, inconsistency, and imprecision of included studies.ConclusionsOrthodontic treatment with aligners is associated with worse treatment outcome compared to fixed appliances in adult patients. Current evidence does not support the clinical use of aligners as a treatment modality that is equally effective to the gold standard of braces.RegistrationPROSPERO (CRD42019131589).
Temporal relations between atrial fibrillation and ischaemic stroke and their prognostic impact on mortality
Authors: Camen Stephan , Ojeda Francisco M , Niiranen Teemu , Gianfagna Francesco , Vishram-Nielsen Julie K , Costanzo Simona , Söderberg Stefan , Vartiainen Erkki , Donati Maria Benedetta , Løchen Maja-Lisa , Pasterkamp Gerard , Magnussen Christina , Kee Frank , Jousilahti Pekka , Hughes Maria , Kontto Jukka , Mathiesen Ellisiv B , Koenig Wolfgang , Palosaari Tarja , Blankenberg Stefan , de Gaetano Giovanni , Jørgensen Torben , Zeller Tanja , Kuulasmaa Kari , Linneberg Allan , Salomaa Veikko , Iacoviello Licia , Schnabel Renate B 
Published: October 2019

Abstract

Aims
Limited evidence is available on the temporal relationship between atrial fibrillation (AF) and ischaemic stroke and their impact on mortality in the community. We sought to understand the temporal relationship of AF and ischaemic stroke and to determine the sequence of disease onset in relation to mortality.

Methods and results
Across five prospective community cohorts of the Biomarkers for Cardiovascular Risk Assessment in Europe (BiomarCaRE) project we assessed baseline cardiovascular risk factors in 100 132 individuals, median age 46.1 (25th–75th percentile 35.8–57.5) years, 48.4% men. We followed them for incident ischaemic stroke and AF and determined the relation of subsequent disease diagnosis with overall mortality. Over a median follow-up of 16.1 years, N = 4555 individuals were diagnosed solely with AF, N = 2269 had an ischaemic stroke but no AF diagnosed, and N = 898 developed both, ischaemic stroke and AF. Temporal relationships showed a clustering of diagnosis of both diseases within the years around the diagnosis of the other disease. In multivariable-adjusted Cox regression analyses with time-dependent covariates subsequent diagnosis of AF after ischaemic stroke was associated with increased mortality [hazard ratio (HR) 4.05, 95% confidence interval (CI) 2.17–7.54; P &lt; 0.001] which was also apparent when ischaemic stroke followed after the diagnosis of AF (HR 3.08, 95% CI 1.90–5.00; P &lt; 0.001).

Conclusion
The temporal relations of ischaemic stroke and AF appear to be bidirectional. Ischaemic stroke may precede detection of AF by years. The subsequent diagnosis of both diseases significantly increases mortality risk. Future research needs to investigate the common underlying systemic disease processes.
Comparing the Slope–Area Threshold for Stream Initiation in Primeval and Managed Forests of Northern Michigan
Authors: Anderson Christopher J 
Published: October 2019

Abstract
Forest management and other land uses can alter hydrological pathways and affect stream initiation along draining hillslopes. To evaluate this potential effect, primeval forests at the Huron Mountain Club in northern Michigan were compared to surrounding forest lands historically logged. A total of 59 stream channel heads (19 in primeval forests and 40 in managed forests) were mapped using GPS. Per the slope–area method, channel heads were plotted within a digital elevation model to determine drainage area and local slope, which were used to discern a threshold of channel initiation. A watershed Hydrologic Soil Index (representing the tendency for surface runoff) was also determined and evaluated for its importance for channel formation. Consistent with the slope–area method, a significant relation was detected between drainage area and local slope for both managed (R2 = .29) and primeval forest watersheds (R2 = .56). However, no significant difference in relation was detected between forest types. This was noteworthy because soils mapped in the primeval forests had a significantly higher Hydrologic Soil Index indicating thinner soils more prone to surface runoff. Results suggest that forest management has likely varied throughout the region but has sustained forest drainage densities comparable to primeval forests.