bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deflating inflation: the connection (or lack thereof) between decisional and metacognitive processes and visual phenomenology
Authors: Abid Greyson 
Published: November 2019

AbstractVision presents us with a richly detailed world. Yet, there is a range of limitations in the processing of visual information, such as poor peripheral resolution and failures to notice things we do not attend. This raises a natural question: How do we seem to see so much when there is considerable evidence indicating otherwise? In an elegant series of studies, Lau and colleagues have offered a novel answer to this long-standing question, proposing that our sense of visual richness is an artifact of decisional and metacognitive deficits. I critically evaluate this proposal and conclude that it rests on questionable presuppositions concerning the relationship between decisional and metacognitive processes, on one hand, and visual phenomenology, on the other.
A general end-to-end diagnosis framework for manufacturing systems
Authors: Yuan Ye , Ma Guijun , Cheng Cheng , Zhou Beitong , Zhao Huan , Zhang Hai-Tao , Ding Han 
Published: November 2019

Abstract
The manufacturing sector is envisioned to be heavily influenced by artificial-intelligence-based technologies with the extraordinary increases in computational power and data volumes. A central challenge in the manufacturing sector lies in the requirement of a general framework to ensure satisfied diagnosis and monitoring performances in different manufacturing applications. Here, we propose a general data-driven, end-to-end framework for the monitoring of manufacturing systems. This framework, derived from deep-learning techniques, evaluates fused sensory measurements to detect and even predict faults and wearing conditions. This work exploits the predictive power of deep learning to automatically extract hidden degradation features from noisy, time-course data. We have experimented the proposed framework on 10 representative data sets drawn from a wide variety of manufacturing applications. Results reveal that the framework performs well in examined benchmark applications and can be applied in diverse contexts, indicating its potential use as a critical cornerstone in smart manufacturing.
Midline Craniotomy for Resection of Cavernous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: November 2019

Abstract
This patient presented with a cavernous malformation in the inferior posterior third ventricle extending into the aqueduct. The patient was positioned supine on the operating room table with the head rotated into the horizontal plane. The choroidal fissure is opened lateral to the choroid plexus. This technique allows for the choroid plexus to serve as protection against forniceal manipulation. Rigid retraction was applied to the cerebral falx and corpus callosum to permit aqueductal visualization. The lighted instruments are paramount for adequate visualization of the third ventricle and during dissection of the lesion. Intraoperative visualization and postoperative imaging confirm gross total resection of the lesion. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute.
Environmental variables driving species and genus level changes in annual plankton biomass
Authors: Forsblom Louise , Engström-öst Jonna , Lehtinen Sirpa , Lips Inga , Lindén Andreas 
Published: November 2019

AbstractAbiotic variables subject to global change are known to affect plankton biomasses, and these effects can be species-specific. Here, we investigate the environmental drivers of annual biomass using plankton data from the Gulf of Finland in the northern Baltic Sea, spanning years 1993–2016. We estimated annual biomass time-series of 31 nanoplankton and microplankton species and genera from day-level data, accounting for the average phenology and wind. We found wind effects on day-level biomass in 16 taxa. We subsequently used state-space models to connect the annual biomass changes with potential environmental drivers (temperature, salinity, stratification, ice cover and inorganic nutrients), simultaneously accounting for temporal trends. We found clear environmental effects influencing the annual biomasses of Dinobryon faculiferum, Eutreptiella spp., Protoperidinium bipes, Pseudopedinella spp., Snowella spp. and Thalassiosira baltica and indicative effects in 10 additional taxa. These effects mostly concerned temperature, salinity or stratification. Together, these 16 taxa represent two-thirds of the summer biomass in the sampled community. The inter-annual variability observed in salinity and temperature is relatively low compared to scenarios of predicted change in these variables. Therefore, the potential impacts of the presented effects on plankton biomasses are considerable.
Diffeomorphisms on the fuzzy sphere
Authors: Ishiki Goro , Matsumoto Takaki 
Published: November 2019

AbstractDiffeomorphisms can be seen as automorphisms of the algebra of functions. In matrix regularization, functions on a smooth compact manifold are mapped to finite-size matrices. We consider how diffeomorphisms act on the configuration space of the matrices through matrix regularization. For the case of the fuzzy $$S^2$, we construct the matrix regularization in terms of the Berezin–Toeplitz quantization. By using this quantization map, we define diffeomorphisms on the space of matrices. We explicitly construct the matrix version of holomorphic diffeomorphisms on $$S^2$. We also propose three methods of constructing approximate invariants on the fuzzy $$S^2$. These invariants are exactly invariant under area-preserving diffeomorphisms and only approximately invariant (i.e. invariant in the large-$$N$ limit) under general diffeomorphisms.
The effects of dietary soybean hulls particle size and diet form on nursery and finishing pig performance1
Authors: Goehring Devin L , Wu Fangzhou , DeRouchey Joel M , Goodband Robert D , Tokach Mike D , Woodworth Jason C , Paulk Chad B , Dritz Steve S 
Published: November 2019

Abstract
Two experiments were conducted to investigate increasing unground and finely ground soybean hulls fed in meal or pelleted form on nursery and finishing pig performance. In experiment 1, 1,100 nursery pigs (initially 6.8 ± 0.1 kg and 28 d of age) were used in a 42-d study with 11 replicates per treatment. Treatments were arranged in a 2 × 2 × 2 factorial with main effects of soybean hulls (10% vs. 20%), grind type (unground, 617 µ vs. ground, 398 µ), and diet type (pelleted vs. meal form). No three-way or soybean hull level × grind type interactions were observed. Overall, average daily gain (ADG) was increased (P &lt; 0.05) by pelleting, decreased (P &lt; 0.05) by grinding, but unaffected by soybean hull levels. Grind type × diet form interactions were observed (P &lt; 0.05) for gain:feed ratio (G:F) and a tendency for average daily feed intake (ADFI; P &lt; 0.10). This was because grinding soybean hulls decreased (P &lt; 0.05) ADFI and increased (P &lt; 0.05) G:F when fed in meal form; however, grinding did not affect ADFI and decreased (P &lt; 0.05) G:F when diets were pelleted. Increasing soybean hulls increased (P &lt; 0.05) ADFI and decreased (P &lt; 0.05) G:F when diets were fed in meal form, but these effects were not observed when diets were pelleted (diet form × soybean hull level interaction, P &lt; 0.06). In experiment 2, 1,215 pigs (initially 21.1 ± 0.1 kg) were used in a 118-d study with nine replications per treatment. Treatments were a corn–soybean meal–based control diet and four diets arranged in a 2 × 2 factorial with the main effects of soybean hulls (7.5% vs. 15%) and grind type (unground, 787 µ vs. ground, 370 µ). All diets were fed in meal form. No soybean hull level × grind type interactions were observed for any growth or carcass responses. Increasing dietary soybean hulls from 0% to 15%, regardless of particle size, did not affect ADG or ADFI, but decreased (linear, P &lt; 0.02) G:F. Carcass yield, hot carcass weight, and backfat depth decreased (linear, P &lt; 0.03) whereas percentage lean increased (linear, P &lt; 0.01) with increasing soybean hulls. Pigs fed ground soybean hulls had increased backfat depth (P &lt; 0.01) and decreased (P &lt; 0.01) percentage lean and fat-free lean index. In summary, increasing soybean hulls up to 20% decreased G:F in nursery and finishing pigs, whereas pelleting nursery diets improved ADG and eliminated the negative effect of increasing soybean hulls on G:F. Grinding soybean hulls reduced growth performance in nursery and finishing pigs.
Drivers of habitat partitioning among three Quercus species along a hydrologic gradient
Authors: Teshera-Levye Jennifer , Miles Brianna , Terwilliger Valery , Lovelock Catherine E , Cavender-Bares Jeannine 
Published: November 2019

Abstract
A critical process that allows multiple, similar species to coexist in an ecological community is their ability to partition local habitat gradients. The mechanisms that underlie this separation at local scales may include niche differences associated with their biogeographic history, differences in ecological function associated with the degree of shared ancestry and trait-based performance differences, which may be related to spatial or temporal variation in habitat. In this study we measured traits related to water-use, growth and stress tolerance in mature trees and seedlings of three oak species (Quercus alba L., Quercus falcata Michx. and Quercus palustris Münchh). which co-occur in temperate forests across the eastern USA but tend to be found in contrasting hydrologic environments. The three species showed significant differences in their local distributions along a hydrologic gradient. We tested three possible mechanisms that influence their contrasting local environmental distributions and promote their long-term co-existence: (i) differences in their climatic distributions across a broad geographic range, (ii) differences in functional traits related to water use, drought tolerance and growth and (iii) contrasting responses to temporal variation in water availability. We identified key differences between the species in both their range-wide climatic distributions (especially aridity index and mean annual temperature) and physiological traits in mature trees and seedlings, including daily water loss, hydraulic conductance, stress responses, growth rate and biomass allocation. Taken together, these differences explain the habitat partitioning that allows three closely related species to co-occur locally.
A “Far North Dixie Land”: Black Settlement, Discrimination, and Community in Urban Alaska
Authors: Hartman Ian C , Reamer David 
Published: November 2019

Abstract
Though it never ranked among the top destinations of the Great Migration, Alaska nevertheless enticed thousands of African Americans during the postwar decades. On the one hand, Black Alaskans experienced the lamentable patterns that defined American race relations in the twentieth century: housing and job discrimination alongside marginalization and racial violence. On the other hand, Black men and women also found in Alaska a place to make their own. This article presents a case study of urban history in the American West and demonstrates that despite its distance from other metropolitan centers, Alaska’s largest city, Anchorage, was not excluded from major postwar trends. Rather, many of the defining through-lines of midcentury U.S. history—mass migration, racial discrimination, community formation, urban planning, and civic activism, to name a few—were present and comprise a dynamic story that until now has never been told.
Melanopsidae (Caenogastropoda: Cerithioidea) from the eastern Mediterranean: another case of morphostatic speciation
Authors: Falniowski Andrzej , Heller Joseph , Cameron Robert A D , Pokryszko Beata M , Osikowski Artur , Rysiewska Aleksandra , Hofman Sebastian 
Published: November 2019

AbstractMelanopsidae were collected from 23 localities in central and south-eastern Europe, the Aegean Islands and Israel. This study considered Melanopsis from the Aegean Islands, the Peloponnese and Israel, and Esperiana esperi, Holandriana holandrii and Microcolpia from continental Europe. Shells and radulae were described and illustrated, showing continuous variation of shell characters and differences in radulae among genera. Phylogenetic analyses were conducted on single-locus datasets (COI, 18S, 28S, ITS2 and H3) and on a concatenated dataset. Molecular data showed a differentiation not paralleled in morphology, reflecting morphostatic evolution. In all species with ribbed shell-forms, the ribbed and unribbed forms did not differ genetically. Within Melanopsis, four clades representing five species were distinguished. Melanopsis buccinoidea is found in Khios and Lesbos Islands, M. astropaliae in Naxos, Samos and Tinos Islands, M. wagneri in Rhodes Island and the Peloponnese, and M. costata and M. saulcyi in Israel. Molecular results and the ICZN rule of priority restrict the range of M. buccinoidea to the North Aegean Islands. ‘Melanopsis’ parreyssi belongs to the genus Microcolpia. Esperiana esperi belongs to a clade separate from Microcolpia.
Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring
Authors: Valle-Inclan Jose Espejo , Stangl Christina , de Jong Anouk C. , van Dessel Lisanne F. , van Roosmalen Markus J. , Helmijr Jean C.A. , Renkens Ivo , de Blank Sam , de Witte Chris J. , Martens John W.M. , Jansen Maurice P.H.M. , Lolkema Martijn P. , Kloosterman Wigard P. 
Published: November 2019

AbstractSomatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of circulating tumor DNA (ctDNA) in liquid biopsies. However, affordable and fast identification of such SV biomarkers is challenging, which hinders routine use in the clinic. Here, we developed a novel approach - termed SHARC - for rapid discovery of somatic SVs as personalized tumor biomarkers. SHARC combines low coverage cancer genome sketching by using Oxford Nanopore sequencing with random forest classification and a dedicated filtering pipeline to enrich for somatic SVs. Our method leverages the real-time and long-read capabilities of nanopore sequencing to identify somatic SV breakpoints at nucleotide resolution from a tumor tissue biopsy within three days. We applied SHARC to tumor samples of high-grade ovarian and prostate cancer and validated on average ten somatic SVs per sample with PCR mini-amplicons. An accompanying method for SV breakpoint detection from liquid biopsies was devised based on digital PCR, enabling detection of cancer in a quantitative manner. Using this method, we retrospectively monitored treatment response in patients with metastatic prostate cancer. Our work demonstrates that SHARC forms a universal framework for rapid development of personalized biomarker assays for blood-based monitoring of any cancer type.
Cellular Fitness Phenotypes of Cancer Target Genes from Oncobiology to Cancer Therapeutics
Authors: George Bijesh , Paul Aswathy Mary , Pillai P. Mukundan , Amjesh Ravikumar , Leitzel Kim , Ali Suhail M. , Sandiford Oleta , Lipton Allan , Rameshwar Pranela , Hortobagyi Gabriel N. , Pillai Madhavan Radhakrishna , Kumar Rakesh 
Published: November 2019

AbstractTo define the growing significance of cellular targets of cancer drugs, we examined the fitness dependency of cellular targets or effectors of cancer drug targets across human cancer cells from 19 cancer types. We observed that the deletion of 35 out of 47 cellular mediators or targets of oncology drugs did not result in the expected loss of cell fitness in appropriate cancer types for which drugs targeting or utilizing these molecules were approved. Additionally, our analysis recognized 43 cellular targets as fitness genes in several cancer types in which these drugs were not approved, and thus, providing clues repurposing approved oncology drugs in cancer types. For example, we found the widespread upregulation and fitness dependency of the components of the mevalonate and purine biosynthesis pathways (currently targeted by bisphosphonates, statins, and pemetrexed in certain cancers) and an association between the overexpression of these targets and reduction in the overall survival duration of patients with breast and other hard-to-treat cancers, for which such drugs are not approved. In brief, the present analysis raised cautions about off-target and undesirable effects of certain oncology drugs in a subset of cancers where the in-tended cellular effectors of drug might not be fitness genes and offers a potential rationale for repurposing certain approved oncology drugs for targeted therapeutics in additional cancer types.
Midbrain activity supports high-level visual properties in primate temporal cortex
Authors: Bogadhi Amarender R. , Katz Leor N. , Bollimunta Anil , Leopold David A. , Krauzlis Richard J. 
Published: November 2019

AbstractThe evolution of the primate brain is marked by a dramatic increase in the number of neocortical areas that process visual information 1. This cortical expansion supports two hallmarks of high-level primate vision – the ability to selectively attend to particular visual features 2 and the ability to recognize a seemingly limitless number of complex visual objects 3. Given their prominent roles in high-level vision for primates, it is commonly assumed that these cortical processes supersede the earlier versions of these functions accomplished by the evolutionarily older brain structures that lie beneath the cortex. Contrary to this view, here we show that the superior colliculus (SC), a midbrain structure conserved across all vertebrates 4, is necessary for the normal expression of attention-related modulation and object selectivity in a newly identified region of macaque temporal cortex. Using a combination of psychophysics, causal perturbations and fMRI, we identified a localized region in the temporal cortex that is functionally dependent on the SC. Targeted electrophysiological recordings in this cortical region revealed neurons with strong attention-related modulation that was markedly reduced during attention deficits caused by SC inactivation. Many of these neurons also exhibited selectivity for particular visual objects, and this selectivity was also reduced during SC inactivation. Thus, the SC exerts a causal influence on high-level visual processing in cortex at a surprisingly late stage where attention and object selectivity converge, perhaps determined by the elemental forms of perceptual processing the SC has supported since before there was a neocortex.
Combining multiple functional connectivity methods to improve causal inferences
Authors: Sanchez-Romero Ruben , Cole Michael W. 
Published: November 2019

AbstractCognition and behavior emerge from brain network interactions, suggesting that causal interactions should be central to the study of brain function. Yet approaches that characterize relationships among neural time series—functional connectivity (FC) methods—are dominated by methods that assess bivariate statistical associations rather than causal interactions. Such bivariate approaches result in substantial false positives since they do not account for confounders (common causes) among neural populations. A major reason for the dominance of methods such as bivariate Pearson correlation (with functional MRI) and coherence (with electrophysiological methods) may be their simplicity. Thus, we sought to identify an FC method that was both simple and improved causal inferences relative to the most popular methods. We started with partial correlation, showing with neural network simulations that this substantially improves causal inferences relative to bivariate correlation. However, the presence of colliders (common effects) in a network resulted in false positives with partial correlation, though this was not a problem for bivariate correlations. This led us to propose a new combined functional connectivity method (combinedFC) that incorporates simple bivariate and partial correlation FC measures to make more valid causal inferences than either alone. We release a toolbox for implementing this new combinedFC method to facilitate improvement of FC-based causal inferences. CombinedFC is a general method for functional connectivity and can be applied equally to resting-state and task-based paradigms.
Solo: doublet identification via semi-supervised deep learning
Authors: Bernstein Nicholas , Fong Nicole , Lam Irene , Roy Margaret , Hendrickson David G. , Kelley David R. 
Published: November 2019

AbstractSingle cell RNA-seq (scRNA-seq) measurements of gene expression enable an unprecedented high-resolution view into cellular state. However, current methods often result in two or more cells that share the same cell-identifying barcode; these “doublets” violate the fundamental premise of single cell technology and can lead to incorrect inferences. Here, we describe Solo, a semi-supervised deep learning approach that identifies doublets with greater accuracy than existing methods. Solo can be applied in combination with experimental doublet detection methods to further purify scRNA-seq data to true single cells beyond any previous approach.
Genetic Deletion of TrpV1 and TrpA1 Does not Alter Avoidance of or Patterns of Brainstem Activation to Citric Acid in Mice
Authors: Yu Tian , Wilson Courtney E. , Stratford Jennifer M. , Finger Thomas E 
Published: November 2019

ABSTRACTExposure of the oral cavity to acidic solutions evokes not only a sensation of sour, but also of sharp or tangy. Acidic substances potentially stimulate both taste buds and acid-sensitive mucosal free nerve endings. Mice lacking taste function (P2X2/P2X3 double-KO mice) refuse acidic solutions similarly to wildtype mice and intraoral infusion of acidic solutions in these KO animals evokes substantial c-Fos activity within orosensory trigeminal nuclei as well as of the nucleus of the solitary tract (nTS) (Stratford et. al 2017). This residual acid-evoked, non-taste activity includes areas that receive inputs from trigeminal and glossopharyngeal peptidergic (CGRP-containing) nerve fibers that express TrpA1 and TrpV1 both of which are activated by low pH. We compared avoidance responses in wildtype (WT) and TrpA1/V1 double KO (TRPA1/V1Db1-/-) mice in brief-access behavioral assay (lickometer) to 1, 3, 10, 30 mM citric acid, along with 100 μM SC45647 and H2O. Both WT and TRPA1/V1Db1-/- show similar avoidance, including to higher concentrations of citric acid (10 and 30 mM; pH 2.62 and pH 2.36 respectively), indicating that neither TrpA1 nor TrpV1 is necessary for the acid avoidance behavior in animals with an intact taste system. Similarly, induction of c-Fos in the nTS and dorsomedial spinal trigeminal nucleus was similar in the WT and TRPA1/V1Db1-/-animals. Taken together these results suggest non-TrpV1 and non-TrpA1 receptors underlie the residual responses to acids in mice lacking taste function.