bluuebunny/crossref_metadata_2025_split huggingface dataset:
Umbilical Cord Blood Lead Level Disparities between Flint and Detroit
Authors: Hanna-Attisha Mona , Gonuguntla Ashweena , Peart Nadine , LaChance Jenny , Taylor D. Kay , Chawla Sanjay 
Published: March 2020

Abstract
Objective The lead-in-water impact of the Flint water crisis on the youngest and most neurodevelopmentally vulnerable population was largely unknown. The objective of this study was to investigate and compare cord blood lead levels (CBLLs) in newborns in Flint, Michigan, after the Flint water crisis, to a group of Detroit newborns.
Study Design Mothers of 99 Flint newborns were surveyed about potential lead exposures. These neonates were born after the recognition of population-wide lead-in-water contamination. CBLLs were measured and maternal–fetal metrics were reviewed. CBLLs and maternal–fetal metrics were then compared with those of a retrospective cohort of 116 Detroit newborns who previously shared the same water source. Analysis involved descriptive statistics, independent t-test, and χ
2 analysis.
Results CBLLs greater than or equal to 1 μg/dL (0.05 μmol/L) were more prevalent among Flint newborns (14%), as compared with Detroit newborns (2%; p = 0.001). This was a sevenfold disparity between Flint and Detroit newborns. No statistically significant differences were found in birth weight, head circumference, small for gestational age status, gestational age, or preterm status among the two groups.
Conclusion The Flint water crisis potentially exposed newborns to lead in utero, implicating maternal–fetal outcomes and future health and development. Primary prevention efforts, including identification and mitigation of lead exposure before conception and during pregnancy, are needed. New environmental exposure detection methods and long-term neurodevelopmental follow-up will complement the findings of this study.
Complement C1q mediates the expansion of periportal hepatic progenitor cells in senescence-associated inflammatory liver
Authors: Ho Tung-Ching , Wang Er-Yea , Yeh Kun-Huei , Jeng Yung-Ming , Horng Jau-Hau , Wu Li-Ling , Chen Yi-Tzu , Huang Hsuan-Cheng , Hsu Chia-Lang , Chen Pei-Jer , Yeh Shiou-Hwei , Chen Ding-Shinn 
Published: March 2020

Significance
This study has identified C1q in the chronic hepatitis liver as an unorthodox signal for activating the essential β-catenin pathway in hepatic progenitor cells (HPCs) and liver tumors, which is critical for their proliferation and dedifferentiation. Inhibition of C1q not only effectively suppressed the expansion, but also facilitated the differentiation of HPCs and liver tumors. However, it spared the orthodox β-catenin function in pericentral normal hepatocytes. C1q thus becomes a potential therapeutic target for liver tumors derived from HPCs in patients with chronic hepatitis.
Navigating graduate school and academia
Authors: Mackey Alison 
Published: March 2020

Abstract
This chapter takes the form of short answers to questions
posed by graduate students. I lay out some of the questions that I have
encountered most frequently during my two decades working with graduate
students as an advisor, as a Director of Graduate Studies, and as an
instructor of a number of classes, including, currently, a Graduate
Professionalization seminar. I also include some of the questions that are
often asked of me by newly graduated students, in their first faculty
positions. I first provide my own answers to these questions, and then point
to the much more complete and focused information that can be found in many
of the other chapters contained in the current volume.
Towards achieving work-life balance in academia
Authors: Larsson Tove , Loewen Shawn , Oliver Rhonda , Sasaki Miyuki , Tracy-Ventura Nicole , Plonsky Luke 
Published: March 2020

Abstract
The competing demands of teaching, research, and service seem
to never end. Consequently, as academics, we often find ourselves feeling
unable to realize our professional goals while also maintaining a life
outside of work. Recognizing that there is no one-size-fits-all way to
achieve or approximate work-life balance, this chapter presents essays on
this topic by five applied linguists with a range of backgrounds. Each is
personal and introspective, providing concrete guidance on what they have
found to be true and helpful in an effort to achieve satisfaction in their
professional as well as personal lives. The chapter also includes an
introduction that brings together five of the main themes found throughout
of the chapter.
Navigating the academic job market
Authors: Long Avizia Y. , Kyle Kristopher , Crookes Graham 
Published: March 2020

Abstract
An important goal for most PhD students is to procure gainful
employment. Although PhD students receive a great deal of training in the
areas of critiquing, conducting, and publishing research, the process of
searching, applying for, and securing an academic job is one that is often
shrouded in mystery. This chapter attempts to shed some light on this
arduous and stressful task, and in doing so make it less mysterious.
Although the chapter is written with PhD students in mind, it may also be
helpful for early career scholars with limited experience on the job market.
Regardless of your individual background/circumstance, training, and
previous job-searching experiences (or lack thereof), the goal is a shared
one: To navigate the academic job market effectively and obtain one or more
job offers. In this chapter, we cover three key phases in the job search
process, including preparing for the job market (as early as possible),
starting the search (approximately one year before one hopes to be
employed), and excelling in job interviews. In each section, we highlight
key aspects of the preparation stage, and provide specific steps an aspiring
academic can take. It is our experience that few reasonably comprehensive
resources exist that provide insight into the entire process of securing an
academic job (see Kelsky, 2015).
Furthermore, few resources offer the joint perspective(s) of new (i.e.,
Avizia and Kris) and seasoned (i.e., Graham) scholars who have successfully
obtained academic jobs in the field. A particular goal of this chapter is to
provide such a resource within the particular context of the field of
applied linguistics.
Antioxidant activity and absorption of cyanidin-3-O-glucoside liposomes in GES-1 cells in vitro
Authors: Quan Zhao , Guan Rongfa , Huang Haizhi , Yang Kai , Cai Ming , Meng Xianghe 
Published: March 2020

ABSTRACT
The use of anthocyanins are limited by their chemical properties. Recent evidence suggests Cyanidin-3-O-glucoside (C3 G) liposomes via the ethanol injection method exhibit improved stability. In the current study, the characterization and cell absorption of C3 G liposomes were explored via transmission electron microscopy and flow cytometry. The internalization of the C3 G liposomes across the gastric epithelial cell monolayer (GES-1 cells) were investigated. Results showed that the particle size and encapsulation efficiency were 234 ± 9.35 nm and 75.0% ± 0.001, respectively. The total antioxidant capacity (T-AOC) and malondialdehyde (MDA) content were used to evaluate the antioxidant activity of C3 G liposomes. The C3 G liposomes can obviously increased T-AOC and decreased the MDA content.Collectively, C3 G liposomes protected human GES-1 cells from gastric mucosal injury induced by H2O2 by activating the related antioxidant pathway. Our research could provide a new effective treatment strategy for the absorption of stomach drugs.
Abbreviations: C3G: Cyanidin-3-O-glucoside; LP: Liposome; GES-1 cells: Human gastric epithelial cell lines; FBS: Fetal Bovine Serum; PBS: Phosphate-buffered saline; PC: Phosphatidylcholine; CH: Cholesterol; MDA: Malondialdehyde; TEM: Transmission electron microscope; FCM: Flow cytometry; FITC: Fluorescein isothiocyanate; DAPI: 4′, 6-diamidino-2phenylidole; FT-IR: Fourier Transform infrared spectroscopy; PFA: Paraformaldehyde
Comparison of CBCT based synthetic CT methods suitable for proton dose calculations in adaptive proton therapy
Authors: Thummerer Adrian , Zaffino Paolo , Meijers Arturs , Marmitt Gabriel Guterres , Seco Joao , Steenbakkers Roel J H M , Langendijk Johannes A , Both Stefan , Spadea Maria F , Knopf Antje C 
Published: March 2020

Abstract
In-room imaging is a prerequisite for adaptive proton therapy. The use of onboard cone-beam computed tomography (CBCT) imaging, which is routinely acquired for patient position verification, can enable daily dose reconstructions and plan adaptation decisions. Image quality deficiencies though, hamper dose calculation accuracy and make corrections of CBCTs a necessity. This study compared three methods to correct CBCTs and create synthetic CTs that are suitable for proton dose calculations. CBCTs, planning CTs and repeated CTs (rCT) from 33 H&N cancer patients were used to compare a deep convolutional neural network (DCNN), deformable image registration (DIR) and an analytical image-based correction method (AIC) for synthetic CT (sCT) generation. Image quality of sCTs was evaluated by comparison with a same-day rCT, using mean absolute error (MAE), mean error (ME), Dice similarity coefficient (DSC), structural non-uniformity (SNU) and signal/contrast-to-noise ratios (SNR/CNR) as metrics. Dosimetric accuracy was investigated in an intracranial setting by performing gamma analysis and calculating range shifts. Neural network-based sCTs resulted in the lowest MAE and ME (37/2 HU) and the highest DSC (0.96). While DIR and AIC generated images with a MAE of 44/77 HU, a ME of −8/1 HU and a DSC of 0.94/0.90. Gamma and range shift analysis showed almost no dosimetric difference between DCNN and DIR based sCTs. The lower image quality of AIC based sCTs affected dosimetric accuracy and resulted in lower pass ratios and higher range shifts. Patient-specific differences highlighted the advantages and disadvantages of each method. For the set of patients, the DCNN created synthetic CTs with the highest image quality. Accurate proton dose calculations were achieved by both DCNN and DIR based sCTs. The AIC method resulted in lower image quality and dose calculation accuracy was reduced compared to the other methods.
Characteristics of ion beams generated in the interaction of ultra-short laser pulses with ultra-thin foils
Authors: McIlvenny A , Ahmed H , Scullion C , Doria D , Romagnani L , Martin P , Naughton K , Sgattoni A , Symes D R , Macchi A , McKenna P , Zepf M , Kar S , Borghesi M 
Published: March 2020

Abstract
Experiments investigating ion acceleration from laser-irradiated ultra-thin foils on the GEMINI laser facility at the Rutherford appleton laboratory indicate a transition to ‘light sail’ radiation pressure acceleration when using circularly polarised, high contrast laser pulses. This paper complements previously published results with additional data and modelling which provide information on the multispecies dynamics taking place during the acceleration, and provides an indication on expected scaling of these processes at higher laser intensities.
Representation of low-tropospheric temperature inversions in ECMWF reanalyses over Europe
Authors: Palarz Angelika , Luterbacher Jürg , Ustrnul Zbigniew , Xoplaki Elena , Celiński-Mysław Daniel 
Published: March 2020

Abstract
Despite the fact that tropospheric temperature inversions are thought to be an important feature of climate as well as a significant factor affecting air quality, low-level cloud formation, and the radiation budget of the Earth, a quantitative assessment of their representation in atmospheric reanalyses is yet missing. Here, we provide new evidence of the occurrence of low-tropospheric temperature inversions and associated uncertainties in their parameters existing among reanalyses produced by the European Centre for Medium-Range Weather Forecasts (ECMWF) and upper-air soundings for Europe covering the period 2001–2010. The reanalyses utilized here include (1) surface-input reanalyses represented by ERA-20C and CERA-20C as well as (2) full-input reanalyses represented by ERA-Interim and ERA5. The upper-air soundings were derived from the Integrated Global Radiosonde Archive (IGRA), version 2. The data consists mainly of air temperature and geopotential height from the model levels (ModLev) and pressure levels (PresLev) of ECMWF reanalyses. The results show that the frequency of surface-based inversions (SBI) and elevated inversions (EI) is largely in agreement among the reanalyses. The quality of their representation depends, however, on the inversion type, season, and region. Over the vast majority of IGRA upper-air stations, SBI frequency is overestimated and EI frequency is underestimated by ECMWF reanalyses. Substantially larger uncertainties arise from the selection between the data of ModLev and PresLev of the reanalyses—the differences in the frequency of the temperature inversions are particularly large for summertime SBI suggesting that PresLev are not capable of resolving the main features of shallow and weak SBI.
Machine learning for the solution of the Schrödinger equation
Authors: Manzhos Sergei 
Published: March 2020

Abstract
Machine learning (ML) methods have recently been increasingly widely used in quantum chemistry. While ML methods are now accepted as high accuracy approaches to construct interatomic potentials for applications, the use of ML to solve the Schrödinger equation, either vibrational or electronic, while not new, is only now making significant headway towards applications. We survey recent uses of ML techniques to solve the Schrödinger equation, including the vibrational Schrödinger equation, the electronic Schrödinger equation and the related problems of constructing functionals for density functional theory (DFT) as well as potentials which enter semi-empirical approximations to DFT. We highlight similarities and differences and specific difficulties that ML faces in these applications and possibilities for cross-fertilization of ideas.
Reporting of Benign Endometrial Cells in Papanicolaou Tests
Authors: Hernandez Andrea , Schatz-Siemers Nina , Zhou Fang , Brandler Tamar C , Negron Raquel , Modi Lopa , Elgert Paul A , Simsir Aylin 
Published: March 2020

Abstract

Objectives
The 2014 Bethesda System (TBS 2014) guidelines for reporting cervical cytology revised the age for reporting benign endometrial cells (BECs) from 40 years or older to age 45 years or older. We evaluated this change and further investigated if extending the reporting age to 50 years or older may be acceptable.

Methods
We reviewed cases with BECs reported on Papanicolaou tests in women age 40 years or older and 45 years or older before and after implementation of TBS 2014. Follow-up endometrial biopsy/curettage results were categorized as benign, endometrial hyperplasia with or without atypia, or malignant. Hyperplasia and malignant follow-up were considered clinically significant. Clinical data were documented. Results were compared for women age 40 to 44, 45 to 49, and 50 years or older.

Results
Follow-up in 15 (100%) women age 40 to 44 years was benign. In women age 45 to 49 years, 61 (96.8%) had benign follow-up, one (1.6%) had atypical hyperplasia, and one (1.6%) had malignant follow-up. In women age 50 years or older, 57 (86.5%) had benign follow-up, four (6%) had malignant follow-up, and seven (7.5%) had atypical or nonatypical hyperplasia. There was a significant difference in follow-up between the age groups of 40 to 49 and 50 or older (P = .023).

Conclusions
We conclude that the TBS 2014 revision was justified. Our data suggest that age 50 years or older rather than age 45 years or older may be an acceptable cutoff for reporting BECs.
Economic Imperception; or, Reading Capital on the Beach with Thoreau
Authors: Moskowitz Alex 
Published: March 2020

AbstractThis essay argues that throughout his oeuvre, Henry David Thoreau develops a theory of sensory perception that comes to its literary culmination in Cape Cod (1865). I argue that Thoreau’s thinking on the senses demonstrates that the senses are a product of historical development. In Cape Cod, Thoreau is particularly interested in how economic interest has trained the senses to become structurally incapable of sensing the death that is a necessary part of the commodity form and social life in general—similar to what Karl Marx in Capital (1867) would describe as “dead labor.” This essay explores how in Cape Cod, Thoreau offers his reader a method of reading that seeks to make legible through literary form—specifically through puns, metaphor, and juxtaposition—the point at which the senses fail. Thoreau’s method in Cape Cod therefore differs from his more well-known works such as Walden (1854), where he only explicitly tells his readers about that to which they are blind. Ultimately, I claim that Thoreau’s political message throughout his career remains much the same, but the way in which he mobilizes literary form to convey that message marks an important change in how we might make sense of—and make sensible—political economy.
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Authors: Weber Cédric R , Akbar Rahmad , Yermanos Alexander , Pavlović Milena , Snapkov Igor , Sandve Geir K , Reddy Sai T , Greiff Victor 
Published: March 2020

Abstract

Summary
B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single and paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis, such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, clustering analysis and machine learning methods for motif detection.

Availability and implementation
The package is available via https://github.com/GreiffLab/immuneSIM and on CRAN at https://cran.r-project.org/web/packages/immuneSIM. The documentation is hosted at https://immuneSIM.readthedocs.io.

Contact
sai.reddy@ethz.ch or victor.greiff@medisin.uio.no

Supplementary information
Supplementary data are available at Bioinformatics online.
A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers
Authors: Rahimi Arezou , Gönen Mehmet 
Published: March 2020

Abstract

Motivation
Genomic information is increasingly being used in diagnosis, prognosis and treatment of cancer. The severity of the disease is usually measured by the tumor stage. Therefore, identifying pathways playing an important role in progression of the disease stage is of great interest. Given that there are similarities in the underlying mechanisms of different cancers, in addition to the considerable correlation in the genomic data, there is a need for machine learning methods that can take these aspects of genomic data into account. Furthermore, using machine learning for studying multiple cancer cohorts together with a collection of molecular pathways creates an opportunity for knowledge extraction.

Results
We studied the problem of discriminating early- and late-stage tumors of several cancers using genomic information while enforcing interpretability on the solutions. To this end, we developed a multitask multiple kernel learning (MTMKL) method with a co-clustering step based on a cutting-plane algorithm to identify the relationships between the input tasks and kernels. We tested our algorithm on 15 cancer cohorts and observed that, in most cases, MTMKL outperforms other algorithms (including random forests, support vector machine and single-task multiple kernel learning) in terms of predictive power. Using the aggregate results from multiple replications, we also derived similarity matrices between cancer cohorts, which are, in many cases, in agreement with available relationships reported in the relevant literature.

Availability and implementation
Our implementations of support vector machine and multiple kernel learning algorithms in R are available at https://github.com/arezourahimi/mtgsbc together with the scripts that replicate the reported experiments.

Supplementary information
Supplementary data are available at Bioinformatics online.
Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
Authors: Sun Kun 
Published: March 2020

Abstract

Motivation
Next-generation sequencing (NGS) data frequently suffer from poor-quality cycles and adapter contaminations therefore need to be preprocessed before downstream analyses. With the ever-growing throughput and read length of modern sequencers, the preprocessing step turns to be a bottleneck in data analysis due to unmet performance of current tools. Extra-fast and accurate adapter- and quality-trimming tools for sequencing data preprocessing are therefore still of urgent demand.

Results
Ktrim was developed in this work. Key features of Ktrim include: built-in support to adapters of common library preparation kits; supports user-supplied, customized adapter sequences; supports both paired-end and single-end data; supports parallelization to accelerate the analysis. Ktrim was ∼2–18 times faster than current tools and also showed high accuracy when applied on the testing datasets. Ktrim could thus serve as a valuable and efficient tool for short-read NGS data preprocessing.

Availability and implementation
Source codes and scripts to reproduce the results descripted in this article are freely available at https://github.com/hellosunking/Ktrim/, distributed under the GPL v3 license.

Contact
sunkun@szbl.ac.cn

Supplementary information
Supplementary data are available at Bioinformatics online.