bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited phenological and pollinator-mediated isolation among selfing and outcrossingArabidopsis lyratapopulations
Authors: Gorman Courtney E. , Bond Lindsay , van Kleunen Mark , Dorken Marcel E. , Stift Marc 
Published: December 2019

AbstractTransitions from outcrossing to selfing have been a frequent evolutionary shift in plants and clearly play a role in species divergence. However, many questions remain about the initial mechanistic basis of reproductive isolation during the evolution of selfing. For instance, how important are prezygotic pre-pollination mechanisms (e.g. changes in phenology and pollinator visitation) in maintaining reproductive isolation between newly arisen selfing populations and their outcrossing ancestors? To test whether changes in phenology and pollinator visitation isolate selfing populations ofArabidopsis lyratafrom outcrossing populations, we conducted a common garden experiment with plants from selfing and outcrossing populations as well as their F1 hybrids. Specifically, we asked whether there was isolation between outcrossing and selfing plants and their F1 hybrids through differences in 1) the timing or intensity of flowering; and/or 2) pollinator visitation. We found that phenology largely overlapped between plants from outcrossing and selfing populations. There were also no differences in pollinator preference related to mating system. Additionally, pollinators preferred to visit flowers on the same plant rather than exploring nearby plants, creating a large opportunity for self-fertilization. Overall, this suggests that prezygotic pre-pollination mechanisms do not strongly reproductively isolate plants from selfing and outcrossing populations ofArabidopsis lyrata.
OCTAVVS: A graphical toolbox for high-throughput preprocessing and analysis of vibrational spectroscopy imaging data
Authors: Troein Carl , Siregar Syahril , Op De Beeck Michiel , Peterson Carsten , Tunlid Anders , Persson Per 
Published: December 2019

AbstractModern vibrational spectroscopy techniques enable rapid collection of thousands of spectra in a single hyperspectral image, allowing researchers to resolve spatially heterogeneous samples down to a resolution of a fewμm. A number of algorithms have been developed to correct for effects such as atmospheric absorption, light scattering by cellular structures and varying baseline levels. Following such preprocessing, spectra are commonly decomposed and clustered to reveal informative patterns and subtle spectral changes. Several of these steps are slow, labor-intensive and require programming skills to make use of published algorithms and code. We here present a free and platform-independent graphical toolbox that allows rapid processing of large sets of spectroscopic images, including atmospheric correction and an algorithm for resonant Mie scattering with improved speed and stability. The software includes modules for decomposition into constituent spectra using the popular MCR-ALS algorithm, augmented by region-of-interest selection, as well as clustering and cluster annotation.
Trajectories of brain volume change over 13 years in chronic schizophrenia
Authors: Barth Claudia , Jørgensen Kjetil N. , Wortinger Laura A. , Nerland Stener , Jönsson Erik G. , Agartz Ingrid 
Published: December 2019

AbstractImportanceSchizophrenia is a leading cause of disability worldwide, with an illness course that putatively deteriorates over time. Whether the notion of a progressive brain disease holds in its chronic stage is debated.ObjectiveTo investigate brain volume change and the impact of iatrogenic factors in chronic schizophrenia patients (duration of illness at baseline 16.17 ± 8.14 years) and controls over 13 years.DesignParticipants were recruited as part of the Human Brain Informatics study. Data acquisition took place between 1999 and 2018, including baseline, 5- and 13-years follow-up.SettingNaturalistic longitudinal case-control study.ParticipantsThe sample consisted of 143 participants, of whom 64 were patients with chronic schizophrenia (20% female, mean age at baseline 40.5 ± 7.7 years) and 79 healthy controls (37% female, mean age at baseline 42.8 ± 8.4 years). T1-weighted structural imaging and information about medication use were obtained at each time point.ExposureAntipsychotic medication and other prescribed drugs.Main Outcome(s) and Measure(s)Individual total and tissue-specific brain volumes, as well as two-time point percentage brain and ventricle volume change.ResultsPatients had lower total brain volume at baseline. Yet, trajectories in total brain volume and gray matter volume loss as well as ventricular enlargement did not differ relative to controls. White matter volume was similar between groups at baseline and 5-year but diverged between 5-year and 13-year follow-up, with accelerated loss in patients. While antipsychotic exposure did not show an association with brain volume loss over time, higher medication load was associated with lower brain volume across time points. Patients on second-generation antipsychotics alone showed lowest total brain volume, only after accounting for add-on drug use.Conclusion and RelevanceWe found limited evidence for progressive brain volume loss in chronic schizophrenia, beyond normal aging. Stable differences in patient brain volumes relative to controls may primarily occur during the first years of illness. All prescribed drugs need to be considered when examining the impact of antipsychotic medication on brain structure.Key PointsQuestionIs chronic schizophrenia associated with progressive brain volume loss beyond normal aging?FindingsWhile brain volume was lower at baseline, patient trajectories of brain volume change over a 13-year follow-up period differed little from healthy individuals. Small effects indicated greater white matter volume loss in patients during the late phase of follow-up. Stable differences in patient brain volumes seem explicable by antipsychotic medication class and respective add-on drugs.MeaningWe found limited evidence of progressive brain volume loss, beyond normal aging, in chronic schizophrenia over 13 years.
Phf15—a novel transcriptional repressor regulating inflammation in mouse microglia
Authors: Muroy Sandra E. , Timblin Greg A. , Preininger Marcela K. , Cedillo Paulina , Saijo Kaoru 
Published: December 2019

AbstractAimExcessive microglial inflammation has emerged as a key player in mediating the effects of aging and neurodegeneration on brain dysfunction. Thus, there is great interest in discovering transcriptional repressors that can control this process. We aimed to examine whetherPhf15—one of the top differentially expressed genes in microglia during aging in humans—could regulate transcription of pro-inflammatory mediators in microglia.MethodsRT-qPCR was used to assessPhf15mRNA expression in mouse brain during aging. Loss-of-function (shRNA-mediated knockdown (KD) and CRISPR/Cas9-mediated knockout (KO) ofPhf15)and gain-of-function (retroviral overexpression (OE) of murinePhf15cDNA) studies in a murine microglial cell line (SIM-A9) followed by immune activation with lipopolysaccharide (LPS) were used to determine the effect ofPhf15on pro-inflammatory factor (Tnfα, Il-1β, Nos2) mRNA expression. RNA-sequencing was used to determine global transcriptional changes afterPhf15knockout under basal conditions and after LPS stimulation.ResultsPhf15expression increases in mouse brain during aging, similar to humans. KD, KO and OE studies determined thatPhf15represses mRNA expression levels of pro-inflammatory mediators such asTnfα, Il-1βandNos2. Global transcriptional changes afterPhf15KO showed thatPhf15specifically represses genes related to the antiviral (type I interferon) response and cytokine production in microglia.ConclusionWe provide the first evidence thatPhf15is an important transcriptional repressor of microglial inflammation, regulating the antiviral response and pro-inflammatory cytokine production. Importantly,Phf15regulates both basal and signal-dependent activation and controls the magnitude and duration of the microglial inflammatory response.
Exploring Food Contents in Scientific Literature with FoodMine
Authors: Hooton Forrest , Menichetti Giulia , Barabási Albert-László 
Published: December 2019

AbstractThanks to the many chemical and nutritional components it carries, diet critically affects human health. However, the currently available comprehensive databases on food composition cover only a tiny fraction of the total number of chemicals present in our food, focusing on the nutritional components essential for our health. Indeed, thousands of other molecules, many of which have well documented health implications, remain untracked. To explore the body of knowledge available on food composition, we built FoodMine, an algorithm that uses natural language processing to identify papers from PubMed that potentially report on the chemical composition of garlic and cocoa. After extracting from each paper information on the reported quantities of chemicals, we find that the scientific literature carries extensive information on the detailed chemical components of food that is currently not integrated in databases. Finally, we use unsupervised machine learning to create chemical embeddings, finding that the chemicals identified by FoodMine tend to have direct health relevance, reflecting the scientific community’s focus on health-related chemicals in our food.
Movement initiation and grasp representation in premotor and primary motor cortex mirror neurons
Authors: S.J. Jerjian , M. Sahani , A. Kraskov 
Published: December 2019

AbstractPyramidal tract neurons (PTNs) within macaque rostral ventral premotor cortex (F5) and primary motor cortex (M1) provide direct input to spinal circuitry and are critical for skilled movement control, but surprisingly, can also be active during passive action observation. We recorded from single neurons, including identified PTNs in the hand and arm area of primary motor cortex (M1) (n=189), and in premotor area F5 (n=115) of two adult male macaques, while they executed, observed, or simply withheld (NoGo) reach-to-grasp and hold actions. We found that F5 maintains a more sustained, similar representation of grasping actions during both execution and observation. In contrast, although some M1 neurons mirrored during the grasp and hold, M1 population activity during observation contained signatures of a withholding state. This suggests that M1 and its output may dissociates signals required for the initiation of movement from those associated with the representation of grasp in order to flexibly guide behaviour.Significance StatementVentral premotor cortex (area F5) maintains a similar representation of grasping actions during both execution and observation. Primary motor cortex and its outputs dissociate between movement and non-movement states.
Design of DNA Origami Diamond Photonic Crystals
Authors: Park Sung Hun , Park Haedong , Hur Kahyun , Lee Seungwoo 
Published: December 2019

AbstractSelf-assembled photonic crystals have proven to be a fascinating class of photonic materials for non-absorbing structural colorizations over large areas and in diverse relevant applications, including tools for on-chip spectrometers and biosensors, platforms for reflective displays, and templates for energy devices. The most prevalent building blocks for the self-assembly of photonic crystals are spherical colloids and block copolymers (BCPs) due to the generic appeal of these materials, which can be crafted into large-area 3D lattices. However, due to the intrinsic limitations of these structures, these two building blocks are difficult to assemble into a direct rod-connected diamond lattice, which is considered to be a champion photonic crystal. Here, we present a DNA origami-route for a direct rod-connected diamond photonic crystal exhibiting a complete photonic bandgap (PBG) in the visible regime. Using a combination of electromagnetic, phononic, and mechanical numerical analyses, we identify (i) the structural constraints of the 50 megadalton-scale giant DNA origami building blocks that could self-assemble into a direct rod-connected diamond lattice with high accuracy, and (ii) the elastic moduli that are essentials for maintaining lattice integrity in a buffer solution. A solution molding process could enable the transformation of the as-assembled DNA origami lattice into a porous silicon- or germanium-coated composite crystal with enhanced refractive index contrast, in that a champion relative bandwidth for the photonic bandgap (i.e., 0.29) could become possible even for a relatively low volume fraction (i.e., 16 vol%).
Prenatal cannabis exposure and childhood outcomes: Results from the ABCD study
Authors: Paul Sarah E. , Hatoum Alexander , Fine Jeremy D. , Johnson Emma C. , Hansen Isabella , Karcher Nicole R. , Moreau Allison L. , Bondy Erin , Qu Yueyue , Carter Ebony B. , Rogers Cynthia E , Agrawal Arpana , Barch Deanna M. , Bogdan Ryan 
Published: December 2019

ABSTRACTImportanceIn light of increasing cannabis use among pregnant women, the Surgeon General of the United States issued an advisory against the use of marijuana during pregnancy on August 29th, 2019.ObjectiveTo determine whether cannabis use during pregnancy is associated with adverse outcomes among offspring.DesignCross-sectional analysis of the baseline session of the ongoing longitudinal Adolescent Brain and Cognitive Development (ABCD) study.SettingData were collected from 22 sites across the United States between 2016 and 2018.ParticipantsChildren ages 9-11 (n=11,489) and their parent or caregiver.ExposurePrenatal marijuana exposure prior to and following maternal knowledge of pregnancy.Main Outcomes and MeasuresChild psychopathology symptomatology (i.e., psychotic-like experiences and internalizing, externalizing, attention, thought, and social problems), cognition, sleep, birth weight, gestational age at birth, body mass index (BMI), and brain structure (i.e., total intracranial volume, white matter volume, gray matter volume). Covariates included familial (e.g., income, familial psychopathology), pregnancy (e.g., prenatal vitamin use, whether the pregnancy was planned), and child (e.g., birth weight, substance use) variables.ResultsAmong 11,489 children (age 9.9±0.6 years; 47.78% female), 655 (5.70%) were prenatally exposed to cannabis in total. Marijuana use prior to (n=648; 5.64%) and following (n=242; 2.11%) maternal knowledge of pregnancy were associated with increased offspring psychopathology characteristics (i.e., psychotic-like experiences and internalizing, externalizing, attention, thought, social, and sleep problems) and BMI as well as reduced cognition, birth weight, and brain structure (i.e., total white and gray mater volumes; all psfdr<.007), but not gestational age at birth. Exposure following maternal knowledge of pregnancy remained significantly associated with psychopathology, cognition, and birth weight outcomes when including potentially confounding variables (all ps<0.046). All associations with exposure prior to maternal knowledge of pregnancy were nonsignificant when considering potentially confounding variables (all ps>0.06).Conclusions and RelevancePrenatal cannabis exposure, and its correlated factors, may increase risk for psychopathology and reduced cognition during middle childhood as well as reduced birthweight. Consistent with recent recommendations by the Surgeon General, marijuana use during pregnancy should be discouraged.
Impact of community treatment with ivermectin for the control of scabies on the prevalence of antibodies to Strongyloides stercoralis in children
Authors: Marks Michael , Gwyn Sarah , Toloka Hilary , Kositz Christian , Asugeni James , Asugeni Rowena , Diau Jason , Kaldor John M , Romani Lucia , Redman-MacLaren Michelle , MacLaren David , Solomon Anthony W , Mabey David CW , Steer Andrew C , Martin Diana 
Published: December 2019

AbstractPrevalence of antibodies to Strongyloides stercoralis was measured in 0–12-year-olds using a bead-based immunoassay before and after ivermectin mass drug administration (MDA) for scabies in the Solomon Islands. Seroprevalence was 9.3% before and 5.1% after MDA (p = 0.019), demonstrating collateral benefits of scabies MDA in this setting.
A Genetically Encoded Trimethylsilyl 1D1H-NMR Probe for Conformation Change in Large Membrane Protein Complexes
Authors: Liu Qi , He Qing-tao , Lyu Xiao-xuan , Yang Fan , Zhu Zhong-liang , Xiao Peng , Yang Zhao , Zhang Feng , Yang Zhao-ya , Wang Xiao-yan , Sun Peng , Wang Qian-wen , Qu Chang-xiu , Gong Zheng , Lin Jing-Yu , Xu Zhen , Song Shao-le , Huang Shen-ming , Guo Sheng-chao , Han Ming-jie , Zhu Kong-kai , Chen Xin , Kahsai Alem W. , Xiao Kun-Hong , Kong Wei , Yu Xiao , Ruan Ke , Li Fa-hui , Niu Xiao-gang , Jin Chang-wen , Wang Jiangyun , Sun Jin-peng 
Published: December 2019

AbstractWhile one dimensional1H nuclear magnetic resonance (1D1H-NMR) spectroscopy is one of the most important and convenient method for measuring conformation change in biomacromolecules, characterization of protein dynamics in large membrane protein complexes by 1D1H-NMR remains challenging, due to the difficulty of spectra assignment, low signal-to-noise ratio (S/N) and the need for large amount of protein. Here we report the site-specific incorporation of 4-trimethylsilyl phenylalanine (TMSiPhe) into proteins, through genetic code expansion inEscherichia colicells, and the measurement of multiple conformational states in membrane protein complex by 1D1H-NMR. The unique up-field1H-NMR chemical shift of TMSiPhe, highly efficient and specific incorporation of TMSiPhe enabled facile assignment of the TMSiPhe1H-NMR signal, and characterization of multiple conformational state in a 150 kilodalton (kD) membrane protein complex, using only 5 μM of protein and 20 min spectra accumulation time. This highly efficient and convenient methods should be broadly applicable for the investigation of dynamic conformation change of protein complexes.
Increased juvenile survival may not be universally linked to longevity: ecological, social and life-history drivers of age-specific mortality in birds
Authors: Mourocq Emeline , Drobniak Szymon M. , Griesser Michael 
Published: December 2019

AbstractA classical prediction of the traditional evolutionary theories of ageing (tETA) is that longevity should be positively correlated with survival early on in life. However, large and unexplained variation exists in juvenile survival-longevity combinations. Here, we provide the first comparative study investigating the life-history, ecological and social correlates of juvenile survival, longevity and their combinations in 204 bird species. Overall, both measurements were positively correlated, but multiple survivals’ combinations evolved, some in accordance with tETA (“positive JS-L combinations”) while others contrasting it (“JS-L mismatches”). Positive JS-L combinations covaried with the pace of life proxies, whereas mismatching combinations covaried with the growing season length, where long growing seasons promoted juvenile survival, while short growing seasons promoted longevity. Interestingly, sociality explained only positive combinations, while life-history and ecological traits explained both positive and mismatching combinations. Overall, these findings challenge a main prediction of the tETA, and identify key evolutionary forces driving the coevolution between juvenile survival and longevity.
Efficient production of saffron crocins and picrocrocin inNicotiana benthamianausing a virus-driven system
Authors: Martí Maricarmen , Diretto Gianfranco , Aragonés Verónica , Frusciante Sarah , Ahrazem Oussama , Gómez-Gómez Lourdes , Daròs José-Antonio 
Published: December 2019

ABSTRACTCrocins and picrocrocin are glycosylated apocarotenoids responsible, respectively, for the color and the unique taste of the saffron spice, known as red gold due to its high price. Several studies have also shown the health-promoting properties of these compounds. However, their high costs hamper the wide use of these metabolites in the pharmaceutical sector. We have developed a virus-driven system to produce remarkable amounts of crocins and picrocrocin in adultNicotiana benthamianaplants in only two weeks. The system consists of viral clones derived from tobacco etch potyvirus that express specific carotenoid cleavage dioxygenase (CCD) enzymes fromCrocus sativusandBuddleja davidii. Metabolic analyses of infected tissues demonstrated that the sole virus-driven expression ofC. sativusCsCCD2L orB. davidiiBdCCD4.1 resulted in the production of crocins, picrocrocin and safranal. Using the recombinant virus that expressed CsCCD2L, accumulations of 0.2% of crocins and 0.8% of picrocrocin in leaf dry weight were reached in only two weeks. In an attempt to improve apocarotenoid content inN. benthamiana, co-expression of CsCCD2L with other carotenogenic enzymes, such asPantoea ananatisphytoene synthase (PaCrtB) and saffron β-carotene hydroxylase 2 (BCH2), was performed using the same viral system. This combinatorial approach led to an additional crocin increase up to 0.35% in leaves in which CsCCD2L and PaCrtB were co-expressed. Considering that saffron apocarotenoids are costly harvested from flower stigma once a year, and thatBuddlejaspp. flowers accumulate lower amounts, this system may be an attractive alternative for the sustainable production of these appreciated metabolites.
Two opposing hippocampus to prefrontal cortex pathways for the control of approach and avoidance behavior
Authors: Sánchez-Bellot Candela , MacAskill Andrew F. 
Published: December 2019

SUMMARYThe decision to either approach or avoid a potentially threatening environment is thought to rely upon complex connectivity between heterogenous neural populations in the ventral hippocampus and prefrontal cortex (PFC). However, how this circuitry can flexibly promote both approach or avoidance at different times has remained elusive. Here, we show that the projection to PFC is composed of two parallel circuits located in the superficial or deep hippocampal pyramidal layers. These circuits have unique upstream and downstream connectivity, and are differentially active during approach and avoidance behavior. The superficial population is preferentially connected to widespread PFC inhibitory interneurons, and its activation promotes exploration; while the deep circuit is connected to PFC pyramidal neurons and fast spiking interneurons, and its activation promotes avoidance. Together this provides a mechanism for regulation of behavior during approach avoidance conflict: through two specialized, parallel circuits that allow bidirectional hippocampal control of PFC.
A novel thermal-visual place learning paradigm for honeybees
Authors: Scheiner R , Frantzmann F , Jäger M , Helfrich-Förster C , Pauls D 
Published: December 2019

AbstractHoneybees have fascinating navigational skills and learning capabilities in the field. To decipher the mechanisms underlying place learning in honeybees, we need paradigms to study place learning of individual honeybees under controlled laboratory conditions. Here, we present a novel visual place learning arena for honeybees which relies on high temperatures as aversive stimuli. Honeybees learn to locate a safe spot in an unpleasantly warm arena, relying on a visual panorama. Bees can solve this task very well at a temperature of 46°C, while at temperatures above 48 °C bees die quickly. This new paradigm, which is based on a pioneering work inDrosophila, allows us now to investigate thermal-visual place learning of individual honeybees in the laboratory, for example after controlled genetic knockout or pharmacological intervention.