156 Works

Additional file 2 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 2. Table S2: Adjuvant treatment information.

Additional file 3 of Vikrahraun—the 1961 basaltic lava flow eruption at Askja, Iceland: morphology, geochemistry, and planetary analogs

Aline Y. Blasizzo, Ingrid A. Ukstins, Stephen P. Scheidt, Alison H. Graettinger, David W. Peate, Tamara L. Carley, Adam J. Moritz & Jennifer E. Thines
Additional file 3: Cumulative chemistry data presented in this paper, including whole-rock chemistry, mineral chemistry, thermometry, and compiled geochemistry of Vikrahraun from the literature

Additional file 5 of Carbohydrates and ginsenosides in shenmai injection jointly improve hematopoietic function during chemotherapy-induced myelosuppression in mice

Shiyu Zhang, Yinxiao Mi, Tingting Ye, Xiaoyan Lu, Li Liu, Jing Qian & Xiaohui Fan
Additional file 5: Table S2. DEGs in Model, S+Rg, S, and Rg groups.

Additional file 8 of Carbohydrates and ginsenosides in shenmai injection jointly improve hematopoietic function during chemotherapy-induced myelosuppression in mice

Shiyu Zhang, Yinxiao Mi, Tingting Ye, Xiaoyan Lu, Li Liu, Jing Qian & Xiaohui Fan
Additional file 8: Table S5. DEGs uniquely regulated in the S+Rg group.

Data from: Meek mothers with powerful daughters: effects of novel host environments and small trait differences on parasitoid competition

Gabriela Hamerlinck, Nathan P. Lemoine, Glen R. Hood, Karen C. Abbott & Andrew A. Forbes
Outcomes of competition may depend both on subtle differences in traits relevant to fitness and on how those traits are expressed in the context of the environment. Environmental effects on traits impacting population dynamics are often overlooked in studies of parasitic wasp (parasitoid) competition. Lineages of the parasitoid Diachasma alloeum (Hymenoptera: Braconidae) differ in relative ovipositor length (a trait affecting the proportion of hosts available for parasitism). Since the size of natal hosts affects the...

Data from: Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum)

Peter R. Wilton, Daniel B. Sloan, John M. Logsdon, Harshavardhan Doddapaneni, Maurine Neiman &
Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in...

Data from: What’s in an outgroup? The impact of outgroup choice on the phylogenetic position of Thalattosuchia (Crocodylomorpha) and the origin of Crocodyliformes

Eric W. Wilberg
Outgroup sampling is a central issue in phylogenetic analysis. However, good justification is rarely given for outgroup selection in published analyses. Recent advances in our understanding of archosaur phylogeny suggest that many previous studies of crocodylomorph and crocodyliform relationships have rooted trees on outgroup taxa that are only very distantly related to the ingroup (e.g., Gracilisuchus stipanicicorum), or might actually belong within the ingroup. Thalattosuchia, a group of Mesozoic marine crocodylomorphs, has a controversial phylogenetic...

Data from: Heterogeneity in genetic diversity among non-coding loci fails to fit neutral coalescent models of population history

Jeffrey L. Peters, Trina E. Robert, Kevin Winker, Kevin G. McCracken & Trina E. Roberts
Inferring aspects of the population histories of species using coalescent analyses of non-coding nuclear DNA has grown in popularity. These inferences, such as divergence, gene flow, and changes in population size, assume that genetic data reflect simple population histories and neutral evolutionary processes. However, violating model assumptions can result in a poor fit between empirical data and the models. We sampled 22 nuclear intron sequences from at least 19 different chromosomes (a genomic transect) to...

Data from: Male offspring production by asexual Potamopyrgus antipodarum, a New Zealand snail

Maurine Neiman, Katelyn Larkin, Andrew R. Thompson & Peter Wilton
As only females contribute directly to population growth, sexual females investing equally in sons and daughters experience a two-fold cost relative to asexuals producing only daughters. Typically, researchers have focused on benefits of sex that can counter this ‘cost of males’ and thus explain its predominance. Here, we instead ask whether asexuals might also pay a cost of males by quantifying the rate of son production in 45 experimental populations (‘lineages’) founded by obligately asexual...

Data from: Tales from the crypt: a parasitoid manipulates the behaviour of its parasite host

Kelly L. Weinersmith, Sean M. Liu, Andrew A. Forbes & Scott P. Egan
There are many examples of apparent manipulation of host phenotype by parasites, yet few examples of hypermanipulation—where a phenotype-manipulating parasite is itself manipulated by a parasite. Moreover, few studies confirm manipulation is occurring by quantifying whether the host's changed phenotype increases parasite fitness. Here we describe a novel case of hypermanipulation, in which the crypt gall wasp Bassettia pallida (a phenotypic manipulator of its tree host) is manipulated by the parasitoid crypt-keeper wasp Euderus set,...

Polychlorinated biphenyl congener data of surficial sediment from Indiana Harbor and Ship Canal, Indiana, USA

Andres Martinez, Karin Norström, Kai Wang & Keri C Hornbuckle
Here, we report the results of the first intensive survey of polychlorinated biphenyls (PCBs) in the surficial sediment of the Indiana Harbor and Ship Canal (IHSC) in East Chicago, Indiana, a part of the Calumet River tributary of Lake Michigan (2006). PCB congeners were measured using tandem mass spectrometry (GC-MS/MS) in multiple reaction monitoring mode (MRM), a method that provides a high-level selectivity and sensitivity for PCBs in complex environmental samples. The PCB concentrations (sum...

Data from: Corollary discharge in precerebellar nuclei of sleeping infant rats

Didhiti Mukherjee, Greta Sokoloff & Mark S. Blumberg
In week-old rats, somatosensory input arises predominantly from external stimuli or from sensory feedback (reafference) associated with myoclonic twitches during active sleep. A previous study suggested that the brainstem motor structures that produce twitches also send motor copies (or corollary discharge, CD) to the cerebellum. We tested this possibility by recording from two precerebellar nuclei—the inferior olive (IO) and lateral reticular nucleus (LRN). In most IO and LRN neurons, twitch-related activity peaked sharply around twitch...

Limits of quantification for individual PCB congeners obtained from 9 blank PUFs analyzed as samples

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle
Determination of LOQ for individual PCB congeners obtained from 6 blank LDPEs analyzed as samples. LOQ calculated from the upper 95% confidence interval

PCB-Kow and PCB-DUow at the IHSC, link to files

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle

Polychlorinated biphenyl concentration in water obtained using passive samplers in IHSC

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle
Individual PCB congener freely-dissolved water concentration, n between 2 and 4, Sampling period 2017-23-05 - 2017-28-06 only one sample, thus std dev = 0.

Polychlorinated biphenyl mass in low density polyethylene obtained using passive samplers in IHSC

Andres Martinez, Andrew M Awad, Nicholas J Herkert & Keri C Hornbuckle

Character data for taxa added to phylogenetic analyses in \"A new crocodylid from the middle Miocene of Kenya and the timing of crocodylian faunal change in the late Cenozoic of Africa\"

Christopher Brochu
Brochuchus is a small crocodylid originally based on specimens from the early Miocene of Rusinga Island, Lake Victoria, Kenya. Here, we report occurrences of Brochuchus from several early and middle Miocene sites. Some are from the Lake Victoria region, and others are in the Lake Turkana Basin. Specimens from the middle Miocene Maboko locality form the basis of a new species, Brochuchus parvidens, which has comparatively smaller maxillary alveoli. Because of the smaller alveoli, the...

Masses of individual polychlorinated biphenyl congeners in particle phases in air in Chicago, Il, USA in 2009

Andres Martinez, Andrew M Awad & Keri C Hornbuckle
We report the levels of airborne individual PCB concentrations of particle phases from the City of Chicago in 2009. Seventeen locations were sampled for particle phases, where 46 particle phases were collected. One hundred and seventy-one individual or coeluting congener PCBs are reported. This dataset includes the sample mass for all 171 individual congeners for particle (QFF) phases, the deployment time and sampling flow.

Tree species of wet tropical forests differ in their tissue biochemistry and effects on soil carbon dynamics

Ann Russell, Rachel Marek & Daniel Olk
Given the hypothesized effects on soil organic matter (SOM) of polyphenols in plant tissues, differences among tree species in their biochemical composition could influence the turnover and accrual of SOM in various ways. The extent to which the biochemical composition of leaf and fine-root tissues differ among tropical tree species, and the effects on soil dynamics, are largely undocumented, however. We used cupric oxide analyses of plant tissues and soil in long-term, replicated, mono-dominant 15-yr-old...

Individual PCB congener masses measured in 24 laboratory blank polyurethane foams (PUFs)

Andres Martinez, Nicholas J Herkert, Jacob C Jahnke & Keri C Hornbuckle
Individual PCB congener mass per PUF from 24 laboratory blanks: PCBs were analyzed using GC-MS/MS.

Blank masses for individual polychlorinated biphenyl congeners in soils from East Chicago, Indiana, USA in 2017/2018

Andres Martinez, Jason Hua, Ezazul Haque, Peter Thorne & Keri C Hornbuckle
Combusted diatomaceous earth (DE, Thermo Fisher Scientific) was used as method blank. A total of 8 method blanks (one blank per sample batch), were included during extraction, clean up and quantification of the samples. Gas chromatography (GC) in tandem with Mass Spectrometry GC-MS/MS (Agilent 7000) in multiple reaction monitoring (MRM) mode was used to quantify all 209 congeners in 171 individual or coeluting congener peaks. The GC was equipped with a Supelco SBP-Octyl capillary column...

Additional file 2 of Mucosal-associated invariant T cells predict increased acute graft-versus-host-disease incidence in patients receiving allogeneic hematopoietic stem cell transplantation

Zhao Wang, Sudong Zhang, Xiaoyu Zhang, Li Liu, Lukun Zhou, Yuyan Shen, Rongli Zhang, Yi He, Donglin Yang, Erlie Jiang, Xiaoming Feng, Jiaxi Zhou, Tao Cheng, Mingzhe Han & Sizhou Feng
Additional file 2: List of differentially expressed gene in RNA-seq.

Additional file 2 of Mucosal-associated invariant T cells predict increased acute graft-versus-host-disease incidence in patients receiving allogeneic hematopoietic stem cell transplantation

Zhao Wang, Sudong Zhang, Xiaoyu Zhang, Li Liu, Lukun Zhou, Yuyan Shen, Rongli Zhang, Yi He, Donglin Yang, Erlie Jiang, Xiaoming Feng, Jiaxi Zhou, Tao Cheng, Mingzhe Han & Sizhou Feng
Additional file 2: List of differentially expressed gene in RNA-seq.

Additional file 3 of Circulating tumor DNA integrating tissue clonality detects minimal residual disease in resectable non-small-cell lung cancer

Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu … & Rong Yin
Additional file 3. Table S3: Performance of three strategies.

Additional file 1 of MetaRNN: differentiating rare pathogenic and rare benign missense SNVs and InDels using deep learning

Chang Li, Degui Zhi, Kai Wang & Xiaoming Liu
Additional file 1: Includes 11 tables for training and testing data sets used in the study. The names of the tables are: Table S1. Training variants for MetaRNN; Table S2. Training variants for MetaRNN-indel; Table S3. Summary statistics for test datasets used to evaluate MetaRNN; Table S4. RNTS validation data set for MetaRNN model evaluation; Table S5. RCTS validation data set for MetaRNN model evaluation; Table S6. AF-RNTS validation data set for MetaRNN model evaluation;...

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