Additional file 2: Table S1. Proteins significantly altered between post versus pre-NACT tissues (LIMMA p-value<0.01). Table S2. Proteins significantly altered between R1 versus R0 patients in pre-NACT tissues (LIMMA p-value<0.05). Table S3. Significantly (LIMMA p<0.05) co-altered proteins between pre-NACT tumors from patients with any level of residual disease vs R0 patients from an independent ovarian cancer cohort (CPTAC 2016) that exhibit highly correlated abundance trends with the present ovarian cancer cohort. Table S4. Diseases and...

Supplementary Figure S1: Multiple sequence alignment of all the ChATPS proteins; Supplementary Table S1: Physicochemical properties of ATPS proteins in C. hupingshanensis. Supplementary Table S2: The gene coding sequences and protein sequences of ChATPS. Supplementary Table S3: Secondary structure analysis of the nine proteins. Supplementary Table S4: Primers used in qRT-PCR analysis for ChATPS. Table S5: The binding energy of each ligand to each protein at the catalytic site (unit: kcal mol-1). Table S6: At...

Additional file 2. Table S2: Adjuvant treatment information.

Supplemental material, sj-xlsx-2-cix-10.1177_11769351221136056 for Optimizing Drug Response Study Design in Patient-Derived Tumor Xenografts by Jessica Weiss, Nhu-An Pham, Melania Pintilie, Ming Li, Geoffrey Liu, Frances A Shepherd, Ming-Sound Tsao and Wei Xu in Cancer Informatics

Abstract Context Genome-wide association studies have identified >450 single nucleotide polymorphisms (SNPs) for type 2 diabetes (T2D). Objective To facilitate use of these SNPs in future genetic risk score (GRS)-based analyses, we aimed to classify the SNPs based on physiology. We also sought to validate GRS associations with insulin-related traits in deeply-phenotyped Mexican Americans. Design, Setting, and Participants 457 T2D SNPs from the literature were assigned physiologic function based on association studies and cluster analyses....

The onset of neurodegenerative diseases activates inflammation that leads to progressive neuronal cell death and impairments in cognition (Alzheimer’s disease, AD) and sight (age-related macular degeneration, AMD). How neuroinflammation can be counteracted is not known. In AMD, amyloid β-peptide (Aβ) accumulates in subretinal drusen. In the 5xFAD retina, we found early functional deficiencies (ERG) without photoreceptor cell (PRC) death and identified early insufficiency in biosynthetic pathways of pro-homeostatic/neuroprotective mediators, neuroprotectin D1 (NPD1) and elovanoids (ELVs)....

Phylogenetic evidence suggests that platyrrhine (or New World) monkeys and caviomorph rodents of the Western Hemisphere derive from source groups from the Eocene of Afro-Arabia, a landmass that was ~1500 to 2000 kilometers east of South America during the late Paleogene. Here, we report evidence for a third mammalian lineage of African origin in the Paleogene of South America—a newly discovered genus and species of parapithecid anthropoid primate from Santa Rosa in Amazonian Perú. Bayesian...

Background. Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping. Methods. Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground...

We use travel-times from a temporary seismic deployment of 30 broadband seismometers and a national catalog of arrival times to construct a finite frequency teleseismic P-wave tomographic model of the upper mantle beneath astern Indonesia, where subduction of the Indo-Australian plate beneath the Banda Arc transitions to arc-continent collision. The change in tectonics is due to a change from oceanic to continental lithosphere in the lower plate as inferred from geologic mapping and geophysical, geochemical,...

This article addresses the challenges in classifying textual data obtained from open online platforms, which are vulnerable to distortion. Most existing classification methods minimize the overall classification error and may yield an undesirably large Type I error (relevant textual messages are classified as irrelevant), particularly when available data exhibit an asymmetry between relevant and irrelevant information. Data distortion exacerbates this situation and often leads to fallacious prediction. To deal with inestimable data distortion, we propose...

In 1967 G.G. Simpson described three partial mandibles from early Miocene deposits in Kenya that he interpreted as belonging to a new strepsirrhine primate, Propotto. This interpretation was quickly challenged, with the assertion that Propotto was not a primate, but rather a pteropodid fruit bat. The latter interpretation has not been questioned for almost half a century. Here we re-evaluate the affinities of Propotto, drawing upon diverse lines of evidence to establish that this strange...

Little is known about the potential for acclimatization or adaptation of corals to ocean acidification and even less about the molecular mechanisms underpinning these processes. Here we examine global gene expression patterns in corals and their intracellular algal symbionts from two replicate population pairs in Papua New Guinea that have undergone long-term acclimatization to natural variation in pCO2. In the coral host, only 61 genes were differentially expressed in response to pCO2 environment, but the...

Microglia are a major cellular component of gliomas, and abundant in the centre of the tumour and at the infiltrative margins. While glioma is a notoriously infiltrative disease, the dynamics of microglia and glioma migratory patterns have not been well characterized. To investigate the migratory behaviour of microglia and glioma cells at the infiltrative edge, we performed two-colour time-lapse fluorescence microscopy of brain slices generated from a platelet-derived growth factor-B (PDGFB)-driven rat model of glioma,...

More than 3000 individual detrital magnetite grains from a fanglomerate near Whitewater (California, USA) were scanned using microCT. These data were used to detect mineral inclusion in these magnetite grains, which can contribute significant amounts of 3He. Grains without inclusions were then picked from these analyzed grains and used to calibrate the cosmogenic 3He production rate in magnetite (manuscript submitted to GChron).

Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their...

Ocean acidification (OA), the global decrease in surface water pH from absorption of anthropogenic CO2, may put many marine taxa at risk. However, populations that experience extreme localized conditions, and are adapted to these conditions predicted in the global ocean in 2100, may be more tolerant to future OA. By identifying locally adapted populations, researchers can examine the mechanisms used to cope with decreasing pH. One oceanographic process that influences pH, is wind driven upwelling....

Chromosomal DNA elements are organized into spatial domains within the eukaryotic nucleus. For example, sites actively undergoing DNA replication, high-level transcription, and repair of double-strand breaks coalesce into foci, although the significance and mechanisms giving rise to these dynamic structures are poorly understood. In S. cerevisiae, replication origins exhibit characteristic subnuclear localizations prior to S phase that anticipate their initiation timing and/or efficiency during S phase: origins found within the nuclear interior in G1 phase...

Subunits of the chromatin remodeler SWI/SNF are the most frequently disrupted genes in cancer. However, how post-translational modifications (PTM) of SWI/SNF subunits elicit epigenetic dysfunction remains unknown. Arginine-methylation of BAF155 by coactivator-associated arginine methyltransferase 1 (CARM1) promotes triple negative breast cancer (TNBC) metastasis. Herein, we discovered the dual roles of methylated-BAF155 (me-BAF155) in promoting tumor metastasis: activation of super-enhanceraddicted oncogenes by recruiting BRD4, and repression of interferon / pathway genes to suppress host immune response....

Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we...

Kissing bugs (Hempitera: Reduviidae) are obligately and exclusively blood feeding insects. Vertebrate blood is thought to provide insufficient B vitamins to insects, which rely on obligate symbiotic relationships with bacteria that provision these nutrients. Kissing bugs harbor environmentally acquired bacteria in their gut lumen, without which they are unable to develop to adulthood. Early experiments identified a single bacterial species, Rhodococcus rhodnii, as a symbiont of Rhodnius prolixus, but modern studies of the kissing bug...

Background: Methamphetamine use is associated with several negative consequences, including neurotoxicity and greater probability of exhibiting a substance use disorder. Sigma1 receptor is involved in the neurobiological basis of several drug use disorders. Cannabidiol has received attention in the treatment of drug use disorders and neurotoxicity. Objectives: To investigate the effects of cannabidiol on methamphetamine-induced conditioned place preference (CPP) and the viability of PC12 cells. Methods: Adult male rats (n = 70) underwent methamphetamine (2...

Additional file 11: Table S4: Proteins with both acetylation and succinylation modifications.

Additional file 4: Table S3. NRAS overexpression induces basal-like features in a human luminal DCIS model SUM225 cells.

Additional file 1: Table S1. Clinical information of study cases. Table S2. Expression of proteins from the PDAC tumors and NATs

Environmental partitioning influences fate, exposure and ecological risks of chemicals. Linear solvation energy relationship (LSER) models may serve as efficient tools for estimating environmental partitioning parameter values that are commonly deficient for many chemicals. Nonetheless, scarcities of empirical solute parameter values of LSER models restricted the application. This study developed and evaluated in silico methods and models to derive the values, in which excess molar refraction, molar volume and logarithm of hexadecane/air partition coefficient were...