bluuebunny/crossref_metadata_2025_split huggingface dataset:
Groping Toward Perversion: From Queer Methods to Queer States in Recent Queer Criticism
Authors: Bascom Ben 
Published: February 2020

Abstract
What’s so queer about the nineteenth century? According to three recent studies of American literature—Elizabeth Freeman’s Beside You in Time (2019), Natasha Hurley’s Circulating Queerness (2018), and Benjamin Kahan’s The Book of Minor Perverts (2019)—the answer may be fairly all encompassing. For these critics, queerness is both an orientation and an object of study, enlivening, engendering, and uncovering a plethora of inchoate possibilities for imagining nonnormativity in the long nineteenth century. As such, these studies help resituate the critical capacity for queer studies to engage with historical material while also attending to the ephemeral possibilities that queerness, as a heuristic, frames, from being a methodology, a narrative trope, or a marker of excess that gets overpassed through dominant and emergent ideologies. Bringing together novels, plays, performances, short stories, and life narratives—along with compelling debates in the fields of queer studies—these books are sure to motivate continued work on the intersections of queerness, affect, and the literary while also plotting ways to consider how queerness disrupts and confirms the biopolitics of sex as a category of analysis.
Mutational analysis indicates that abnormalities in rhizobial infection and subsequent plant cell and bacteroid differentiation in pea (Pisum sativum) nodules coincide with abnormal cytokinin responses and localization
Authors: Dolgikh Elena A , Kusakin Pyotr G , Kitaeva Anna B , Tsyganova Anna V , Kirienko Anna N , Leppyanen Irina V , Dolgikh Aleksandra V , Ilina Elena L , Demchenko Kirill N , Tikhonovich Igor A , Tsyganov Viktor E 
Published: February 2020

AbstractBackground and AimsRecent findings indicate that Nod factor signalling is tightly interconnected with phytohormonal regulation that affects the development of nodules. Since the mechanisms of this interaction are still far from understood, here the distribution of cytokinin and auxin in pea (Pisum sativum) nodules was investigated. In addition, the effect of certain mutations blocking rhizobial infection and subsequent plant cell and bacteroid differentiation on cytokinin distribution in nodules was analysed.MethodsPatterns of cytokinin and auxin in pea nodules were profiled using both responsive genetic constructs and antibodies.Key ResultsIn wild-type nodules, cytokinins were found in the meristem, infection zone and apical part of the nitrogen fixation zone, whereas auxin localization was restricted to the meristem and peripheral tissues. We found significantly altered cytokinin distribution in sym33 and sym40 pea mutants defective in IPD3/CYCLOPS and EFD transcription factors, respectively. In the sym33 mutants impaired in bacterial accommodation and subsequent nodule differentiation, cytokinin localization was mostly limited to the meristem. In addition, we found significantly decreased expression of LOG1 and A-type RR11 as well as KNOX3 and NIN genes in the sym33 mutants, which correlated with low cellular cytokinin levels. In the sym40 mutant, cytokinins were detected in the nodule infection zone but, in contrast to the wild type, they were absent in infection droplets.ConclusionsIn conclusion, our findings suggest that enhanced cytokinin accumulation during the late stages of symbiosis development may be associated with bacterial penetration into the plant cells and subsequent plant cell and bacteroid differentiation.
A path recorder algorithm for Multiple Longest Common Subsequences (MLCS) problems
Authors: Wei Shiwei , Wang Yuping , Yang Yuanchao , Liu Sen 
Published: February 2020

Abstract

Motivation
Searching the Longest Common Subsequences of many sequences is called a Multiple Longest Common Subsequence (MLCS) problem which is a very fundamental and challenging problem in many fields of data mining. The existing algorithms cannot be applicable to problems with long and large-scale sequences due to their huge time and space consumption. To efficiently handle large-scale MLCS problems, a Path Recorder Directed Acyclic Graph (PRDAG) model and a novel Path Recorder Algorithm (PRA) are proposed.

Results
In PRDAG, we transform the MLCS problem into searching the longest path from the Directed Acyclic Graph (DAG), where each longest path in DAG corresponds to an MLCS. To tackle the problem efficiently, we eliminate all redundant and repeated nodes during the construction of DAG, and for each node, we only maintain the longest paths from the source node to it but ignore all non-longest paths. As a result, the size of the DAG becomes very small, and the memory space and search time will be greatly saved. Empirical experiments have been performed on a standard benchmark set of both DNA sequences and protein sequences. The experimental results demonstrate that our model and algorithm outperform the related leading algorithms, especially for large-scale MLCS problems.

Availability and implementation
This program code is written by the first author and can be available at https://www.ncbi.nlm.nih.gov/nuccore and https://blog.csdn.net/wswguilin.

Supplementary information
Supplementary data are available at Bioinformatics online.
Breeze: an integrated quality control and data analysis application for high-throughput drug screening
Authors: Potdar Swapnil , Ianevski Aleksandr , Mpindi John-Patrick , Bychkov Dmitrii , Fiere Clément , Ianevski Philipp , Yadav Bhagwan , Wennerberg Krister , Aittokallio Tero , Kallioniemi Olli , Saarela Jani , Östling Päivi 
Published: February 2020

Abstract

Summary
High-throughput screening (HTS) enables systematic testing of thousands of chemical compounds for potential use as investigational and therapeutic agents. HTS experiments are often conducted in multi-well plates that inherently bear technical and experimental sources of error. Thus, HTS data processing requires the use of robust quality control procedures before analysis and interpretation. Here, we have implemented an open-source analysis application, Breeze, an integrated quality control and data analysis application for HTS data. Furthermore, Breeze enables a reliable way to identify individual drug sensitivity and resistance patterns in cell lines or patient-derived samples for functional precision medicine applications. The Breeze application provides a complete solution for data quality assessment, dose–response curve fitting and quantification of the drug responses along with interactive visualization of the results.

Availability and implementation
The Breeze application with video tutorial and technical documentation is accessible at https://breeze.fimm.fi; the R source code is publicly available at https://github.com/potdarswapnil/Breeze under GNU General Public License v3.0.

Contact
swapnil.potdar@helsinki.fi

Supplementary information
Supplementary data are available at Bioinformatics online.
Trade-offs between burrowing and biting force in fossorial scincid lizards?
Authors: Le Guilloux Margot , Miralles Aurélien , Measey John , Vanhooydonck Bieke , O’Reilly James C , Lowie Aurélien , Herrel Anthony 
Published: February 2020

AbstractTrade-offs are thought to be important in constraining evolutionary divergence as they may limit phenotypic diversification. The cranial system plays a vital role in many functions including defensive, territorial, predatory and feeding behaviours in addition to housing the brain and sensory systems. Consequently, the morphology of the cranial system is affected by a combination of selective pressures that may induce functional trade-offs. Limbless, head-first burrowers are thought to be constrained in their cranial morphology as narrow heads may provide a functional advantage for burrowing. However, having a wide and large head is likely beneficial in terms of bite performance. We used 15 skink species to test for the existence of trade-offs between maximal push and bite forces, and explored the patterns of covariation between external head and body morphology and performance. Our data show that there is no evidence of a trade-off between bite and burrowing in terms of maximal force. Species that generate high push forces also generate high bite forces. Our data also show that overall head size covaries with both performance traits. However, future studies exploring trade-offs between force and speed or the energetic cost of burrowing may reveal other trade-offs.
Platysace (Apiaceae) of south-western Australia: silent story tellers of an ancient human landscape
Authors: Lullfitz Alison , Byrne Margaret , Knapp Lynette , Hopper Stephen D 
Published: February 2020

AbstractHigh gene flow and a population structure corresponding to human rather than geographical drivers are likely to be genetic patterns of human-dispersed plant taxa. We examined variation in geographical structure and gene flow estimates based on three non-coding regions of plastid DNA in three south-west Australian members of the Platysace genus to identify whether a human influence on dispersion of utilized taxa was detectable. Edible tubers of Platysace deflexa and Platysace trachymenioides have been harvested historically by Noongar traditional owners, whereas Platysace effusa has no known cultural significance. We found differences between utilized and non-utilized taxa, particularly when considered against the generally complex phylogeographical patterning in south-west Australian plant taxa. Platysace effusa showed a pattern of high population divergence, low gene flow and multiple refugia, consistent with a long evolutionary history, past climatic oscillations and persistence in a highly fragmented landscape. In contrast, higher gene flow estimates, less divergence between populations and common haplotypes in P. deflexa and in P. trachymenioides over the south-eastern part of its range are consistent with anthropogenic influences. This study contributes to the understanding of human influences on south-west Australian plant taxa that have been present since the late Pleistocene, but to date have received little scientific attention.
Hydrological and thermal responses of seeds from four co-occurring tree species from southwest Western Australia
Authors: Rajapakshe Rajapakshe P V G S W , Turner Shane R , Cross Adam T , Tomlinson Sean 
Published: February 2020

AbstractSeed germination is a critical stage in the life cycle of most plants and is defined by specific tolerance thresholds beyond which rates and success of germination rapidly decline. Previous studies have demonstrated that widespread plant species commonly germinate over a broad range of temperatures and water stress levels, whereas range-restricted species often exhibit a narrower germination window in terms of temperature and moisture. We investigated the relationships of the key germination traits of maximum germination (Gmax) and time to 50% germination (t50) in response to temperature (5–35°C) and water stress (−1.5–0 MPa) in four co-occurring Western Australian native Eucalyptus species with widely varying biogeography. Eucalyptus caesia subsp. caesia and E. ornata exhibit a highly localized distribution and a narrow geographical range, being restricted either to granite outcrops or the upper slopes and tops of lateritic rises, respectively. These two species were compared with the two widespread and dominant congenerics E. salmonophloia and E. salubris. There was a distinctive hump-shaped response of t50 to temperature and an exponential response to water stress, characteristic of rate- and threshold-limited processes, but no consistent pattern in the response of Gmax. The four species were significantly different in their thermal performance of t50, with E. caesia and E. ornata displaying narrower thermal tolerance ranges than the two widespread species. In terms of mean final germination percentage, the two range-restricted endemic taxa exhibited higher lability in their response to thermal stress and drought stress compared to the two broadly distributed congenerics. These findings indicate a link between distributional extent, temperature and water stress tolerance and may have implications for identifying ecological filters of rarity and endemism.
Artificial intelligence deciphers codes for color and odor perceptions based on large-scale chemoinformatic data
Authors: Zhang Xiayin , Zhang Kai , Lin Duoru , Zhu Yi , Chen Chuan , He Lin , Guo Xusen , Chen Kexin , Wang Ruixin , Liu Zhenzhen , Wu Xiaohang , Long Erping , Huang Kai , He Zhiqiang , Liu Xiyang , Lin Haotian 
Published: February 2020

Abstract

Background
Color vision is the ability to detect, distinguish, and analyze the wavelength distributions of light independent of the total intensity. It mediates the interaction between an organism and its environment from multiple important aspects. However, the physicochemical basis of color coding has not been explored completely, and how color perception is integrated with other sensory input, typically odor, is unclear.

Results
Here, we developed an artificial intelligence platform to train algorithms for distinguishing color and odor based on the large-scale physicochemical features of 1,267 and 598 structurally diverse molecules, respectively. The predictive accuracies achieved using the random forest and deep belief network for the prediction of color were 100% and 95.23% ± 0.40% (mean ± SD), respectively. The predictive accuracies achieved using the random forest and deep belief network for the prediction of odor were 93.40% ± 0.31% and 94.75% ± 0.44% (mean ± SD), respectively. Twenty-four physicochemical features were sufficient for the accurate prediction of color, while 39 physicochemical features were sufficient for the accurate prediction of odor. A positive correlation between the color-coding and odor-coding properties of the molecules was predicted. A group of descriptors was found to interlink prominently in color and odor perceptions.

Conclusions
Our random forest model and deep belief network accurately predicted the colors and odors of structurally diverse molecules. These findings extend our understanding of the molecular and structural basis of color vision and reveal the interrelationship between color and odor perceptions in nature.
Back to the future: five forgotten lessons for the healthcare managers of today
Authors: Gibiino Giovanni , Rugo Michele , Maffoni Marina , Giardini Anna 
Published: February 2020

AbstractNowadays, political, economic and technological upheavals require the rediscovery of some elapsed soft skills by healthcare managers. These abilities are values grounded in the past and somewhat nebulous in the present. We suggest five forgotten lessons highlighting the importance of a stronger human and self-conscious approach in today’s and tomorrow’s healthcare managers.
A15 MICROBES MEDIATE FIBER-INDUCED INFLAMMATION IN IBD
Authors: Armstrong H , Dickner R , Rieger A , Mander I K , Jerasi J , Santer D , Valcheva R , Dijk S I , Petrova A , Dieleman L A , Carroll M W , Huynh H Q , Wine E 
Published: February 2020

Abstract

Background
The etiology of inflammatory bowel diseases (IBD) remains unknown, although gut microorganisms and diet have been implicated. Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, promoting gut health. However, many IBD patients describe experiencing sensitivity to fibres. Interestingly, fiber receptors on immune cells are able to interact with fibers typically found on the surface of fungal cells (which share properties with dietary fibers), for example, resulting in a paradoxical pro-inflammatory response.

Aims
As an altered microbial composition is a hallmark of IBD, we hypothesized that the loss of fiber fermenting-microbes populating the IBD gut could lead to dietary fibers not being efficiently broken down into their beneficial biproducts, resulting in binding of intact fibers to pro-inflammatory host cell receptors. This can ultimately drive pro-inflammatory responses and a microenvironment that promotes continued dysbiosis and increased pathogenicity of select microbes, as observed in IBD.

Methods
Fiber receptor expression gut was examined using immunohistochemistry and flow cytometry and demonstrated elevated receptor expression due to increased presence of immune cells in IBD patient biopsies. Cytokine secretion, in response to fiber (5mg/mL) or pre-fermented fibers, cultured with microbes of interest, was measured by ELISAs in cell lines in vitro and biopsy tissues cultured ex vivo.

Results
Whole-fibers induced pro-inflammatory cytokine production in macrophage, monocytes, and neutrophils. Specific microbes were capable of fermenting fiber, measured by gas chromatography. Pre-fermentation of fibers by these microbes reduced inflammatory cytokine production. The fiber oligofructose increased IL-1β in pediatric CD (n=44) and UC (n=29) biopsies cultured ex vivo but not in non-IBD (n=25). The increase was greater in patients with more severe disease. Pre-fermentation of oligofructose by bacteria reduced this secretion of IL-1β. Whole-microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce fiber-associated inflammation in macrophage cells compared to remission or non-IBD children. Statistical analysis of food frequency questionnaire (FFQ) data on fiber consumption demonstrated that fiber-associated inflammation in patient biopsies cultured ex vivo (ELISA and qPCR) correlated with fiber avoidance (FFQ).

Conclusions
Comparing in vitro findings to our patient FFQs, intestinal washes (microbe abundance), and detailed patient history will better define the relationship between microbes, dietary fibers, and gut inflammation in IBD. This will allow for tailored dietary intervention through dietary recommendations, prebiotic, and/or probiotic therapies.

Funding Agencies
CCCWeston Foundation, WCHRI
A30 INHIBITION OF NF-KB SIGNALING IN DCLK1+ CELLS PROMOTES COLONIC INFLAMMATION AND COLITIS-ASSOCIATED CANCER
Authors: Good H , Shin A E , Zhang L , Asfaha S 
Published: February 2020

Abstract

Background
Colorectal cancer (CRC) is the 2nd leading cause of cancer death in Canada. A major risk factor for this disease is chronic inflammation. Despite the clear link between inflammation and cancer, the exact mechanism by which colitis leads to cancer is unknown. Our group has previously shown that a rare cell type in the gut marked by the expression of doublecortin-like kinase-1 (Dclk1) and known as a tuft cell, is quiescent, long-lived, and resistant to proliferation even upon mutation of the tumor suppressor APC. Interestingly, in the setting of colitis, these APC-mutated tuft cells become powerful cancer-initiating cells, but the mechanism by which this occurs is not known. NF-kB signaling is a major inflammatory pathway active in colitis and that has been linked to colorectal cancer. Inhibition of the NF-kB pathway in intestinal epithelial cells has also been shown to inhibit tumor initiation in a mouse model of colitis-associated cancer (Greten et al., 2004).

Aims
In the present study, we aim to examine the effect of NF-kB inhibition in tuft cells on colitis-associated cancer.

Methods
Dclk1CreERT2/APCf/f mice were crossed to IKK-β f/f mice and administered tamoxifen to conditionally knockout the function of both APC and IKK-β in tuft cells. Mice were then exposed to the colitis-inducing agent dextran sodium sulfate (DSS) to induce tumorigenesis. Approximately 16 weeks post-tamoxifen, colonic tumor number and size were analyzed to determine the effect of NF-kB pathway inhibition on tumor initiation and growth, respectively. Extent of inflammation was assessed by myeloperoxidase (MPO) activity and histological damage, and colonic tissue was collected for measurement of inflammatory mediators by qRT-PCR at both acute and long-term time points.

Results
Interestingly, at baseline we detected increased MPO activity in Dclk1CreERT2/APCf/f/IKK-β f/f mice compared to control mice, suggesting that inhibition of NF-kB in Dclk1+ cells may increase basal colonic inflammation. Consistent with this observation, inhibition of the NF-kB pathway also resulted in an increased number of tuft cell-derived tumors, with no observed change in tumor size. Acutely, we also observed an exacerbation of DSS-colitis in Dclk1CreERT2/APCf/f/IKK-β f/f mice, as detected by elevated MPO activity, increased histological damage, and reduced colon length compared to wildtype (IKK-β +/+) controls.

Conclusions
These data suggest that Dclk1+ cell-specific NF-kB signaling plays a key protective role against colitis and colitis-associated tumorigenesis. Targeting the NF-kB pathway may reduce the severity of colitis and the incidence of colitis-associated cancer.

Funding Agencies
CIHR
A32 THE REGULATION OF INTESTINAL SMOOTH MUSCLE CELL PROLIFERATION IN CROHN’S DISEASE – IS NR4A1 A NOVEL TARGET TO TREAT FIBROSTENOSIS?
Authors: Szczepanski H , Tsai Y , Venu V P , Alston L , Hirota S A 
Published: February 2020

Abstract

Background
Intestinal fibrosis and stricture formation are common complications of Crohn’s disease (CD). Recently, the stricturing phenotype has been recognized to be primarily attributable to hypertrophy/hyperplasia of smooth muscle, rather than an increase in fibrosis alone. Despite advances in treatment of CD, current therapies do little to prevent or reverse strictures. NR4A1 is an orphan nuclear receptor that has been reported as anti-fibrotic in non-intestinal systems and exhibits anti-proliferative effects in smooth muscle cells (SMCs). NR4A1 gene variants have been associated with increased risk of IBD, however, the mechanisms regulating NR4A1 expression and its role in intestinal SMC function has not been investigated.

Aims
To characterize and understand the role of NR4A1 activation in the regulation of mitogen-induced proliferation of intestinal SMCs.

Methods
Primary intestinal SMCs were isolated from Nr4a1+/+ and Nr4a1-/- mice. Furthermore, a commercially sourced human primary intestinal SMC line was used. To assess the response of SMCs to culture and identify growth differences, proliferation was measured via trypan blue exclusion and EdU incorporation. In mouse and human SMCs, proliferation was induced by platelet-derived growth factor-BB (PDGF-BB) and NR4A1 activation was assessed by pretreating with selective agonists, cytosporone B (Csn-B) and 6-mercaptopurine (6-MP), at various concentrations. Mass spectrometry was used to characterize proteomic differences between Nr4a1+/+ and Nr4a1-/- SMCs. Expression levels of NR4A1 were assessed by qPCR and western blot after mitogen exposure and Csn-B treatment.

Results
Nr4a1-/- cells exhibited a significantly higher rate of proliferation compared to Nr4a1+/+ cells, under both basal and mitogen-exposed conditions. Proteomic analysis showed that Nr4a1-/- SMCs exhibited increased expression of proteins related to the cell cycle and metabolism, compared to Nr4a1+/+ SMCs. Pretreating human intestinal SMCs with Csn-B and 6-MP significantly attenuated proliferation induced by PDGF-BB. Similar effects were observed in Nr4a1+/+ SMCs, however, the anti-proliferative effect of Csn-B was absent in Nr4a1-/- cells. Furthermore, NR4A1 expression was rapidly induced by Csn-B and PDGF-BB, the latter response suggesting the existence of a potential negative feedback mechanism to control mitogen-induced SMC proliferation.

Conclusions
Our results suggest that NR4A1 is a critical regulator of intestinal SMC proliferation and its induction by mitogens may contribute to a negative feedback loop to control smooth muscle growth. These data support targeting NR4A1 to treat excessive smooth muscle hypertrophy/hyperplasia that contributes to tissue remodelling observed in fibrostenotic CD.

Funding Agencies
CAG, CCC, CIHR