bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiplicity functions of quasars: predictions from the MassiveBlackII simulation
Authors: Bhowmick Aklant K , Di Matteo Tiziana , Myers Adam D
Published: January 2020

We examine multiple active galactic nucleus (AGN) systems (triples and quadruples, in particular) in the MassiveBlackII simulation over a redshift range of 0.06 ≲ z ≲ 4. We identify AGN systems (with bolometric luminosity $L_{\mathrm{bol}}\gt 10^{42}~\mathrm{erg\, s}^{-1}$) at different scales (defined by the maximum distance between member AGNs) to determine the AGN multiplicity functions. This is defined as the volume/surface density of AGN systems per unit richness R, the number of AGNs in a system. We find that gravitationally bound multiple AGN systems tend to populate scales of ${\lesssim}0.7~\mathrm{cMpc}\, h^{-1}$; this corresponds to angular separations of ≲100 arcsec and a line-of-sight velocity difference ${\lesssim}200~\mathrm{km\, s}^{-1}$. The simulation contains ∼10 and ∼100 triples/quadruples per deg2 up to depths of DESI (g ≲ 24) and LSST (g ≲ 26) imaging, respectively; at least $20{{\ \rm per\ cent}}$ of these should be detectable in spectroscopic surveys. The simulated quasar ($L_{\mathrm{bol}}\gt 10^{44}~\mathrm{erg\, s}^{-1}$) triples and quadruples predominantly exist at 1.5 ≲ z ≲ 3. Their members have black hole masses $10^{6.5}\lesssim M_{\mathrm{ bh}}\lesssim 10^{9}~\mathrm{M}_{\odot }\, h^{-1}$ and live in separate (one central and multiple satellite) galaxies with stellar masses $10^{10}\lesssim M_{*}\lesssim 10^{12}~\mathrm{M}_{\odot }\, h^{-1}$. They live in the most massive haloes (e.g. ${\sim}10^{13}~\mathrm{M}_{\odot }\, h^{-1}$ at z = 2.5; ${\sim}10^{14}~\mathrm{M}_{\odot }\, h^{-1}$ at z = 1) in the simulation. Their detections provide an exciting prospect for understanding massive black hole growth and their merger rates in galaxies in the era of multimessenger astronomy.
A large, deep 3 deg2 survey of H α, [O iii], and [O ii] emitters from LAGER: constraining luminosity functions
Authors: Khostovan A A , Malhotra S , Rhoads J E , Jiang C , Wang J , Wold I , Zheng Z-Y , Barrientos L F , Coughlin A , Harish S , Hu W , Infante L , Perez L A , Pharo J , Valdes F , Walker A R , Yang H
Published: January 2020

We present our measurements of the H α, [O iii], and [O ii] luminosity functions as part of the Lyman Alpha Galaxies at Epoch of Reionization (LAGER) survey using our samples of 1577 z = 0.47 H α-, 3933 z = 0.93 [O iii]-, and 5367 z = 1.59 [O ii]-selected emission line galaxies in a 3 deg2 single, CTIO/Blanco DECam pointing of the COSMOS field. Our observations reach 5σ depths of 8.2 × 10−18 erg s−1 cm−2 and comoving volumes of (1−7) × 105 Mpc3 making our survey one of the deepest narrow-band surveys. We select our emission line galaxies via spectroscopic confirmation, photometric redshifts, and colour–colour selections. We measure the observed luminosity functions for each sample and find best fits of $\phi ^\star = 10^{-3.16^{+0.09}_{-0.09}}$ Mpc−3 and $L^\star = 10^{41.72^{+0.09}_{-0.09}}$ erg s−1 for H α, $\phi ^\star = 10^{-2.16^{+0.10}_{-0.12}}$ Mpc−3 and $L^\star = 10^{41.38^{+0.07}_{-0.06}}$ erg s−1 for [O iii], and $\phi ^\star = 10^{-1.97^{+0.07}_{-0.07}}$ Mpc−3 and $L^\star = 10^{41.66^{+0.03}_{-0.03}}$ erg s−1 for [O ii], with α fixed to −1.75, −1.6, and −1.3, respectively. An excess of bright >1042 erg s−1 [O iii] emitters is observed and may be due to active galactic nucleus (AGN) contamination. Corrections for dust attenuation are applied assuming AHα = 1 mag. We also design our own empirical rest-frame g − r calibration using SDSS DR12 data, test it against our z = 0.47 H α emitters with zCOSMOS 1D spectra, and calibrate it for (g − r) between −0.8 and 1.3 mag. Dust and AGN-corrected star formation rate densities (SFRDs) are measured as log10ρSFR/(M⊙ yr−1 Mpc−3) = −1.63 ± 0.04, −1.07 ± 0.06, and −0.90 ± 0.10 for H α, [O iii], and [O ii], respectively. We find our [O iii] and [O ii] samples fully trace cosmic star formation activity at their respective redshifts in comparison to multiwavelength SFRDs, while the H α sample traces ∼70 per cent of the total z = 0.47 SFRD.
The identification of novel mutations in PLCZ1 responsible for human fertilization failure and a therapeutic intervention by artificial oocyte activation
Authors: Mu Jian , Zhang Zhihua , Wu Ling , Fu Jing , Chen Biaobang , Yan Zheng , Li Bin , Zhou Zhou , Wang Wenjing , Zhao Lin , Dong Jie , Kuang Yanping , Sun Xiaoxi , He Lin , Wang Lei , Sang Qing
Published: January 2020

Fertilization involves a series of molecular events immediately following egg–sperm fusion; Ca2+ oscillations are the earliest signaling event, and they initiate the downstream reactions including pronucleus formation. Successful human reproduction requires normal fertilization. In clinical IVF or ICSI attempts, some infertile couples suffer from recurrent fertilization failure. However, the genetic reasons for fertilization failure are largely unknown. Here, we recruited several couples diagnosed with fertilization failure even though their gametes are morphologically normal. Through whole-exome sequencing and Sanger sequencing, we identified biallelic mutations in gene-encoding phospholipase C zeta 1 (PLCZ1) in four independent males in couples diagnosed with fertilization failure. Western blotting showed that missense mutations decreased the level of PLCZ1 and that nonsense or frameshift mutations resulted in undetectable or truncated proteins. Expression of these mutations in mice significantly reduced the levels of oocyte activation. Artificial oocyte activation in patient oocytes could rescue the phenotype of fertilization failure and help establish pregnancy and lead to live birth. Our findings expand the spectrum of PLCZ1 mutations that are responsible for human fertilization failure and provide a potentially feasible therapeutic treatment for these patients.
Biphasic unbinding of a metalloregulator from DNA for transcription (de)repression in Live Bacteria
Authors: Jung Won , Sengupta Kushal , Wendel Brian M , Helmann John D , Chen Peng
Published: January 2020

Microorganisms use zinc-sensing regulators to alter gene expression in response to changes in the availability of zinc, an essential micronutrient. Under zinc-replete conditions, the Fur-family metalloregulator Zur binds to DNA tightly in its metallated repressor form to Zur box operator sites, repressing the transcription of zinc uptake transporters. Derepression comes from unbinding of the regulator, which, under zinc-starvation conditions, exists in its metal-deficient non-repressor forms having no significant affinity with Zur box. While the mechanism of transcription repression by Zur is well-studied, little is known on how derepression by Zur could be facilitated. Using single-molecule/single-cell measurements, we find that in live Escherichia coli cells, Zur's unbinding rate from DNA is sensitive to Zur protein concentration in a first-of-its-kind biphasic manner, initially impeded and then facilitated with increasing Zur concentration. These results challenge conventional models of protein unbinding being unimolecular processes and independent of protein concentration. The facilitated unbinding component likely occurs via a ternary complex formation mechanism. The impeded unbinding component likely results from Zur oligomerization on chromosome involving inter-protein salt-bridges. Unexpectedly, a non-repressor form of Zur is found to bind chromosome tightly, likely at non-consensus sequence sites. These unusual behaviors could provide functional advantages in Zur's facile switching between repression and derepression.
Programmable deformation of patterned bimorph actuator swarm
Authors: Ma Jia-Nan , Zhang Yong-Lai , Han Dong-Dong , Mao Jiang-Wei , Chen Zhao-Di , Sun Hong-Bo
Published: January 2020

Graphene-based actuators featuring fast and reversible deformation under various external stimuli are promising for soft robotics. However, these bimorph actuators are incapable of complex and programmable 3D deformation, which limits their practical application. Here, inspired from the collective coupling and coordination of living cells, we fabricated a moisture-responsive graphene actuator swarm that has programmable shape-changing capability by programming the SU-8 patterns underneath. To get better control over the deformation, we fabricated SU-8 micropattern arrays with specific geometries and orientations on a continuous graphene oxide film, forming a swarm of bimorph actuators. In this way, predictable and complex deformations, including bending, twisting, coiling, asymmetric bending, 3D folding, and combinations of these, have been achieved due to the collective coupling and coordination of the actuator swarm. This work proposes a new way to program the deformation of bilayer actuators, expanding the capabilities of existing bimorph actuators for applications in various smart devices.
Why do Adolescents Initiate and Continue Using Tobacco and Areca Nut?: A Qualitative Study Tracing Pathways of Use Among School-Going Adolescents in Mumbai, India
Authors: Gupte Himanshu A , D’Costa Marina , Chaudhuri Leni
Published: January 2020

Background

Tobacco and areca-nut use among adolescents has been reported from different parts of India. Multiple factors influence initiation of tobacco use among adolescents. Initiation of one product gradually extends to multiple products. Studies on initiation lack documentation of the pathways and experiences post-initiation, which is required to holistically understand behavior patterns of adolescents for planning timely intervention. This study was conducted to trace pathways and identify factors influencing the initiation and continuation of tobacco and areca-nut among adolescents.

Methods

In this two-staged study, we conducted 14 focus group discussions (FGDs) with 166 adolescents studying in grades 7–9 (11–18 years) from six municipal schools in Mumbai, India. They had self-reported areca-nut or smoked or smokeless tobacco (SLT) use. Pathways of initiation were traced through in-depth interviews for 60 adolescents.

Results

Four multi-linear pathways of use were identified: (1) areca-nut only, (2) areca-nut to tobacco, (3) initiation with SLT, and (4) initiation with smoking. Raw or sweetened areca-nut, betel leaf, gutka, masheri, mawa, hookah, cigarette, bidi, and e-cigarettes were products reported to be used. Curiosity, easy access to tobacco products and normalization of tobacco use influenced initiation. Areca-nut acted as a precursor to tobacco use.

Conclusion

Tracing pathways in tobacco use helped to understand reasons for initiation, influences in continuation of use, and experiences of significance to the adolescents. Experiences of adolescents play a critical role in shaping the pathways of tobacco use. Understanding the pathways and influencers will further help to build effective health promotion communication, policies for sale to minors, and school-based cessation interventions.

Implications

Findings of the study provide an insight into unknown areas of information regarding products used by adolescents, their patterns of consumption, perceptions, and their pathways of initiation and continuation of primary and secondary products. This will help in developing specific public health awareness messages, policies regarding packaging and sale of areca-nut to children and interventions targeted for the adolescents and their specific products of use not just in India but for the South-East Asia region as areca-nut and tobacco use among adolescents is common in the region. The exercise of tracing the pathways provides basis for cessation counseling among adolescents.
Hypophosphataemic osteomalacia due to cadmium exposure in the silver industry
Authors: Paul J , Cherian K E , Thomas N , Paul T V
Published: January 2020

Chronic heavy metal exposure and the health hazards that ensue are important public-health problems. We highlight the occurrence of hypophosphataemic osteomalacia due to chronic cadmium exposure in the silver industry in India. Three silversmiths presented similarly with clinical, biochemical and radiological evidence of hypophosphataemic osteomalacia. Considering their occupation, their blood samples were screened for heavy metals and were found to have toxic levels of cadmium. They were initiated on neutral phosphate and calcitriol. On follow-up, they reported significant reduction in severity of symptoms. It is essential to maintain a high index of suspicion in diagnosing this condition. A thorough knowledge of the occupational background of patients, as well as ambient conditions at the workplace is of utmost importance in contemplating the possibility of such rare occurrences. Moreover, regulatory agencies and policy makers ought to survey the silver industry and ensure that the metals used are within permissible safe limits of exposure.
Isolation of highly selective IgNAR variable single-domains against a human therapeutic Fc scaffold and their application as tailor-made bioprocessing reagents
Authors: Buschhaus Magdalena J , Becker Stefan , Porter Andrew J , Barelle Caroline J
Published: January 2020

The adaptive immune system of cartilaginous fish (Elasmobranchii), comprising of classical hetero-tetrameric antibodies, is enhanced through the presence of a naturally occurring homodimeric antibody-like immunoglobulin—the new antigen receptor (IgNAR). The binding site of the IgNAR variable single-domain (VNAR) offers advantages of reduced size (<1/10th of classical immunoglobulin) and extended binding topographies, making it an ideal candidate for accessing cryptic epitopes otherwise intractable to conventional antibodies. These attributes, coupled with high physicochemical stability and amenability to phage display, facilitate the selection of VNAR binders to challenging targets. Here, we explored the unique attributes of these single domains for potential application as bioprocessing reagents in the development of the SEED-Fc platform, designed to generate therapeutic bispecific antibodies. A panel of unique VNARs specific to the SEED homodimeric (monospecific) ‘by-products’ were isolated from a shark semi-synthetic VNAR library via phage display. The lead VNAR candidate exhibited low nanomolar affinity and superior selectivity to SEED homodimer, with functionality being retained upon exposure to extreme physicochemical conditions that mimic their applicability as purification agents. Ultimately, this work exemplifies the robustness of the semi-synthetic VNAR platform, the predisposition of the VNAR paratope to recognise novel epitopes and the potential for routine generation of tailor-made VNAR-based bioprocessing reagents.
Like-for-like bibliometric substitutes for peer review: Advantages and limits of indicators calculated from the ep index
Authors: Rodríguez-Navarro Alonso , Brito Ricardo
Published: January 2020

The use of bibliometric indicators would simplify research assessments. The 2014 Research Excellence Framework (REF) is a peer review assessment of UK universities, whose results can be taken as benchmarks for bibliometric indicators. In this study, we use the REF results to investigate whether the ep index and a top percentile of most cited papers could substitute for peer review. The probability that a random university’s paper reaches a certain top percentile in the global distribution of papers is a power of the ep index, which can be calculated from the citation-based distribution of university’s papers in global top percentiles. Making use of the ep index in each university and research area, we calculated the ratios between the percentage of 4-star-rated outputs in REF and the percentages of papers in global top percentiles. Then, we fixed the assessment percentile so that the mean ratio between these two indicators across universities is 1.0. This method was applied to four units of assessment in REF: Chemistry, Economics and Econometrics joined to Business and Management Studies, and Physics. Some relevant deviations from the 1.0 ratio could be explained by the evaluation procedure in REF or by the characteristics of the research field; other deviations need specific studies by experts in the research area. These results indicate that in many research areas the substitution of a top percentile indicator for peer review is possible. However, this substitution cannot be made straightforwardly; more research is needed to establish the conditions of the bibliometric assessment.
Dysbalanced Resting-State Functional Connectivity Within the Praxis Network Is Linked to Gesture Deficits in Schizophrenia
Authors: Wüthrich Florian , Viher Petra V , Stegmayer Katharina , Federspiel Andrea , Bohlhalter Stephan , Vanbellingen Tim , Wiest Roland , Walther Sebastian
Published: January 2020

Patients with schizophrenia frequently present deficits in gesture production and interpretation, greatly affecting their communication skills. As these gesture deficits can be found early in the course of illness and as they can predict later outcomes, exploring their neural basis may lead to a better understanding of schizophrenia. While gesturing has been reported to rely on a left lateralized network of brain regions, termed praxis network, in healthy subjects and lesioned patients, studies in patients with schizophrenia are sparse. It is currently unclear whether within-network connectivity at rest is linked to gesture deficit. Here, we compared the functional connectivity between regions of the praxis network at rest between 46 patients and 44 healthy controls. All participants completed a validated test of hand gesture performance before resting-state functional magnetic resonance imaging (fMRI) was acquired. Patients performed gestures poorer than controls in all categories and domains. In patients, we also found significantly higher resting-state functional connectivity between left precentral gyrus and bilateral superior and inferior parietal lobule. Likewise, patients had higher connectivity from right precentral gyrus to left inferior and bilateral superior parietal lobule (SPL). In contrast, they exhibited lower connectivity between bilateral superior temporal gyrus (STG). Connectivity between right precentral gyrus and left SPL, as well as connectivity between bilateral STG, correlated with gesture performance in healthy controls. We failed to detect similar correlations in patients. We suggest that altered resting-state functional connectivity within the praxis network perturbs correct gesture planning in patients, reflecting the gesture deficit often seen in schizophrenia.
Intellectual property, institutional dynamics, and firm innovation
Authors: Zhou William Chongyang , Wang Ruicheng
Published: January 2020

The relationship between intellectual property (IP) and innovation has been discussed extensively in extant literature. However, the dynamic essence of IP as an institutional context, particularly its setback and reversal, has received little attention. Through the lens of institutional dynamics theory, this study identifies four asymmetric categories of IP institutional dynamics: accelerating reforms, decaying reforms, decaying reversals, and accelerating reversals in a typical emerging market, China. Favorable institutional dynamics (i.e. accelerating reforms and decaying reversals) improve firms’ R&D efficiency, whereas unfavorable institutional dynamics (i.e. decaying reforms and accelerating reversals) reduce R&D efficiency. Moreover, R&D input decreases in an unfavorable institutional context.
A cross-sectional study of periportal fibrosis and Schistosoma mansoni infection among school-aged children in a hard-to-reach area of Madagascar
Authors: Russell Hannah J , Penney James M StJ , Linder Cortland , Joekes Elizabeth C , Bustinduy Amaya L , Stothard J Russell , Rakotomampianina Daniel A L , Andriamasy Emmanuel H , Mahary Lalarizo R , Ranjanoro Elodie P , Rahetilahy Alain M , Spencer Stephen A
Published: January 2020

Background

A cross-sectional survey was performed to estimate the prevalence of periportal fibrosis in children based on ultrasound examination in the Marolambo district of the Atsinanana region of Madagascar. This is a remote area known to have a high prevalence of intestinal schistosomiasis.

Methods

School-aged children (5–14 y) were selected from six villages for parasitological and sonographic examination. Circulating cathodic antigen (CCA) tests and Kato Katz (KK) stool microscopy were performed. Video-clips of liver views were recorded with a SonoSite iViz and interpreted in the UK by comparison with standardised images (WHO protocol).

Results

The prevalence of schistosomiasis according to CCA testing was 97.8% (269/275) and 73.8% (203/275) by KK. Sonographic evidence of periportal fibrosis was observed in 11.3% (31/275). The youngest children with fibrosis were aged 6 y. Fibrosis was more common in older children (p=0.03) but was not associated with either infection intensity category (p=0.07) or gender (p=0.67).

Conclusions

Findings of periportal fibrosis among children in these hard-to-reach villages suggests chronic Schistosoma mansoni infection from a very young age. This may reflect other similarly remote schistosomiasis-endemic areas and reinforces the need to investigate morbidity in neglected communities to understand the true extent of disease burden in endemic countries.
Combined Use of Trichoderma atroviride CCTCCSBW0199 and Brassinolide to Control Botrytis cinerea Infection in Tomato
Authors: Li Ting-ting , Zhang Jing-di , Tang Jia-quan , Liu Zhi-cheng , Li Ya-qian , Chen Jie , Zou Li-wen
Published: January 2020

Tomato gray mold caused by Botrytis cinerea is one of the main diseases of tomato and significantly impacts the yield and quality of tomato fruit. The overuse of chemical fungicides has resulted in the development of fungicide-resistant strains. Biological control is becoming an alternative method for the control of plant diseases to replace or decrease the application of traditional synthetic chemical fungicides and genus Trichoderma is widely used as a biological agent for controlling tomato gray mold. Brassinolide (BR) is a plant-growth-promoting steroid. To enhance the efficiency and stability of Trichoderma activity against B. cinerea, an optimal combination of Trichoderma atroviride CCTCCSBW0199 and BR that controls B. cinerea infection in tomato was identified. Strain CCTCCSBW0199 was found to have antagonistic activity against B. cinerea both in vitro and in vivo. In addition, a fermented culture of chlamydospores and metabolites, or metabolites only of strain CCTCCSBW0199 also reduced growth of B. cinerea. BR reduced growth of B. cinerea and had no effect on the sporulation and growth of Trichoderma spp. An application of metabolites of a Trichoderma sp. + BR reduced gray mold on tomato leaves by approximately 70.0%. Furthermore, the activities of induced defense response-related enzyme, such as peroxidase, superoxide dismutase, catalase, and phenylalanine ammonia-lyase were increased in tomato plants treated with a Trichoderma sp. + BR. Our data suggested that applying a mix of metabolites of T. atroviride CCTCCSBW0199 + BR was effective at reducing gray mold of tomato and may lay a theoretical foundation for the development of novel biofungicides.
Sterol Demethylation Inhibitor Fungicide Resistance in Leptosphaeria maculans is Caused by Modifications in the Regulatory Region of ERG11
Authors: Yang Yongqing , Marcoft Stephen J. , Forsyth Leanne M. , Zhao Ji , Li Ziqin , Van de Wouw Angela P. , Idnurm Alexander
Published: January 2020

Blackleg is a worldwide disease of canola (Brassica napus), caused by a complex of fungal species in the genus Leptosphaeria, that impacts canola production and seed quality. Demethylation inhibitor (DMI) fungicides that target sterol 14α-demethylase are an integral part of disease control. Here, we report six DMI-resistant isolates of Leptosphaeria maculans and two different types of genetic modification related to the resistance. Analysis of the regulatory region of the DMI target gene ERG11 (also known as CYP51) revealed a 275-bp insertion in two of the isolates and three long terminal repeat retrotransposons (5,263, 5,267, and 5,248 bp) inserted in the promoter region of three resistant isolates. Genetic approaches confirmed that these elements are responsible for DMI resistance in L. maculans and crosses show segregation consistent with a single locus. Reverse-transcription quantitative PCR assays demonstrated that the 275-bp insertion increases ERG11 gene expression, conferring DMI fungicide resistance both in vitro and in planta. Moreover, transformation of a susceptible isolate of L. maculans with ERG11 driven by a promoter containing the 275-bp insertion increased resistance to tebuconazole. A minimal shift of the values of concentration whereby 50% of the mycelial growth is inhibited in vitro was observed in resistant isolates containing long terminal repeat retrotransposons; nevertheless, these isolates were able to develop significant lesions on cotyledons from fungicide-treated seedlings. This is the first report of genetic modifications in L. maculans relating to DMI fungicide resistance.
Identification of Stripe Rust Resistance Genes in Common Wheat Cultivars From the Huang-Huai-Hai Region of China
Authors: Huang Liang , Xiao Xing Zhi , Liu Bo , Gao Li , Gong Guo Shu , Chen Wan Quan , Zhang Min , Liu Tai Guo
Published: January 2020

Wheat stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious fungal disease worldwide, especially in the Huang-Huai-Hai region, a main wheat production area in China. Gene postulation, molecular testing, and pedigree analysis were conducted to determine the presence of stripe rust resistance genes to 15 Pst races in 66 selected commercial wheat cultivars released from 2000 to 2016. In addition, races CYR32, CYR33, and CYR34 were used to evaluate resistance to Pst at the adult-plant stage of wheat in the field. Four Yr genes (Yr9, Yr10, Yr26, and Yr32) were postulated in 24 wheat cultivars either singly or in combination. Thirty-six cultivars might contain unknown Yr genes, whereas no identified Yr gene was postulated in six cultivars. Yr9 was detected at a frequency of 28.8%, and no cultivars carried Yr5, Yr15, or Yr18. Ten cultivars (15.2%) exhibited adult-plant resistance in the field tests with three predominant races. Three cultivars (Langyan 43, Xinong 889, and Yunfeng 139) had all-stage resistance. These results are useful to growers selecting cultivars and to breeders aiming to use more resistance genes to develop new cultivars with effective resistance in order to reduce stripe rust damage.
Compassion and Health Care: A Discussion With the Dalai Lama
Authors: Snyderman Ralph , Gyatso Tenzin
Published: January 2020

The calling to be a physician has historically been driven by compassion—that is, the desire to relieve the suffering of others. However, the current health care delivery system in the United States has increasingly limited the ability of physicians to express compassion as they are afforded little time for meaningful interaction with their patients. One of the authors (R.S.) draws on his current focus on developing personalized, proactive, and patient-driven models of care to argue that patient engagement plays a critical role in achieving favorable outcomes. Believing that compassion is key for establishing the physician–patient relationship needed to foster patient engagement, R.S. sought the advice of one of the world’s most recognized thought leaders on this topic, His Holiness the 14th Dalai Lama. This Invited Commentary describes the meeting between the two authors, the Dalai Lama’s thoughts about compassion, and his challenge to bring attention to the importance of compassion in medical education, practice, and research.
Pupillary Abnormalities in Descemet Membrane Endothelial Keratoplasty After Nearly Full Tamponade
Authors: Arnalich-Montiel Francisco , Pérez-Sarriegui Ane , Lauzirika Gorka , Porrua Laura , Hernández-Verdejo José Luis
Published: January 2020

Purpose:

To describe the incidence, risk factors, and management of pupillary abnormalities after anterior chamber (AC) full air or gas tamponade in Descemet membrane endothelial keratoplasty (DMEK) without pupillary block.

Methods:

In this retrospective case series, clinical records of 25 patients (32 eyes) who underwent DMEK were reviewed for pupillary abnormalities and iris morphology. All patients had nearly full intracameral tamponade with air or 20% SF6 at the end of surgery without default air release postoperatively.

Results:

Pupillary abnormalities ranging from mild ovalization to mid-mydriasis were seen in 56% of the cases. These abnormalities were not related to morphometric changes in the iris volume, or in the iris dilator or iris sphincter muscle, but were probably due to posterior synechiae. Combining DMEK and cataract surgery increases by 5-fold the odds of developing this complication. Surgical revision of the posterior surface of the iris and synechiolysis reversed these pupillary abnormalities.

Conclusions:

Nonischemic pupillary abnormalities can be seen in patients with DMEK using a nearly full air/gas tamponade in the AC after surgery despite patent iridectomy especially when combined with cataract surgery. Ensuring complete mydriasis in the immediate postoperative period and a free-floating bubble in the AC above the inferior pupillary margin may reduce its incidence.
Pediatric Gastroesophageal Reflux Clinical Practice Guidelines: Joint Recommendations of the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN)
Authors: Vandenplas Yvan , Rudolph Colin D ,   Committee Members:, Di Lorenzo Carlo , Hassall Eric , Liptak Gregory , Mazur Lynnette , Sondheimer Judith , Staiano Annamaria , Thomson Michael , Veereman‐Wauters Gigi , Wenzl Tobias G
Published: January 2020

Objective:

To develop a North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition (NASPGHAN) and European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) international consensus on the diagnosis and management of gastroesophageal reflux and gastroesophageal reflux disease in the pediatric population.

Methods:

An international panel of 9 pediatric gastroenterologists and 2 epidemiologists were selected by both societies, which developed these guidelines based on the Delphi principle. Statements were based on systematic literature searches using the best‐available evidence from PubMed, Cumulative Index to Nursing and Allied Health Literature, and bibliographies. The committee convened in face‐to‐face meetings 3 times. Consensus was achieved for all recommendations through nominal group technique, a structured, quantitative method. Articles were evaluated using the Oxford Centre for Evidence‐based Medicine Levels of Evidence. Using the Oxford Grades of Recommendation, the quality of evidence of each of the recommendations made by the committee was determined and is summarized in appendices.

Results:

More than 600 articles were reviewed for this work. The document provides evidence‐based guidelines for the diagnosis and management of gastroesophageal reflux and gastroesophageal reflux disease in the pediatric population.

Conclusions:

This document is intended to be used in daily practice for the development of future clinical practice guidelines and as a basis for clinical trials.
Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field
Authors: Lee Jae-Chan , Whang Kyung-Sook
Published: January 2020

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family

Intrasporangiaceae

showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family

Intrasporangiaceae

, for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).
Sphingomonas solaris sp. nov., isolated from a solar panel in Boston, Massachusetts
Authors: Tanner Kristie , Mancuso Christopher P. , Peretó Juli , Khalil Ahmad S. , Vilanova Cristina , Pascual Javier
Published: January 2020

Solar panel surfaces, although subjected to a range of extreme environmental conditions, are inhabited by a diverse microbial community adapted to solar radiation, desiccation and temperature fluctuations. This is the first time a new bacterial species has been isolated from this environment. Strain R4DWNT belongs to the genus

Sphingomonas

and was isolated from a solar panel surface in Boston, MA, USA. Strain R4DWNT is a Gram-negative, non-motile and rod-shaped bacteria that tested positive for oxidase and catalase and forms round-shaped, shiny and orange-coloured colonies. It is mesophilic, neutrophilic and non-halophilic, and presents a more stenotrophic metabolism than its closest neighbours. The major fatty acids in this strain are C18:1ω7c/C18:1ω6c, C16:1ω7c/C16:1ω6c﻿, C14:0 2OH and C16:0. Comparison of 16S rRNA gene sequences revealed that the closest type strains to R4DWNT are

Sphingomonas fennica

,

Sphingomonas formosensis

,

Sphingomonas prati

,

Sphingomonas montana

and

Sphingomonas oleivorans

with 96.3, 96.1, 96.0, 95.9 and 95.7 % pairwise similarity, respectively. The genomic G+C content of R4DWNT is 67.9 mol%. Based on these characteristics, strain R4DWNT represents a novel species of the genus

Sphingomonas

for which the name Sphingomonas solaris sp. nov. is proposed with the type strain R4DWNT (=CECT 9811T=LMG 31344T).
BioSkills Guide: Development and National Validation of a Tool for Interpreting the Vision and Change Core Competencies
Authors: Clemmons Alexa W , Timbrook Jerry , Herron Jon C , Crowe Alison J
Published: January 2020

To excel in modern STEM careers, biology majors need a range of transferrable skills, yet competency development is often a relatively underdeveloped facet of the undergraduate curriculum. Here, we have elaborated the Vision and Change core competency framework into a resource called the BioSkills Guide, a set of measurable learning outcomes that can be more readily interpreted and implemented by faculty. College biology educators representing over 250 institutions, including 73 community colleges, contributed to the development and validation of the guide. Our grassroots approach during the development phase engaged over 200 educators over the course of five iterative rounds of review and revision. We then gathered evidence of the BioSkills Guide’s content validity using a national survey of over 400 educators. Across the 77 outcomes in the final draft, rates of respondent support for outcomes were high (74.3% - 99.6%). Our national sample included college biology educators across a range of course levels, subdisciplines of biology, and institution types. We envision the BioSkills Guide supporting a variety of applications in undergraduate biology, including backward design of individual lessons and courses, competency assessment development, curriculum mapping and planning, and resource development for less well-defined competencies.
Ecological patterns of root nodule diversity in cultivated and wild rooibos populations: a community prediction approach
Authors: Ramoneda Josep , Le Roux Jaco , Frossard Emmanuel , Frey Beat , Gamper Hannes Andres
Published: January 2020

There is interest in understanding the factors behind the biogeography of root-associated bacteria due to the joint effects that plant host, climate, and soil conditions can have on bacterial diversity. For legume crops with remaining wild populations, this is of even more importance, because the effects of cropping on undisturbed root-associated bacterial communities can be addressed. Here, we used a community prediction approach to describe the diversity of the root nodule bacterial communities of rooibos (Aspalathus linearis), an endemic legume crop from South Africa. The goal was to reveal whether patterns of root nodule community composition in paired cultivated and wild rooibos populations could be related to geographical distance, plant traits, and plant population type (i.e. cultivated or uncultivated). We identified a core of dominant and widespreadMesorhizobiumZOTUs that each defined one of 4 different root nodule community classes. Rooibos cultivation impacted root nodule bacterial diversity at regional and local scales, while the geographical origin of the root nodule communities was the strongest predictor of root nodule community structure. Beyond impacts of cultivation on root nodule bacterial diversity, this study suggests a mixture of dispersal limitation and ecological drift regionally, and selection by different plant populations locally, define the biogeography of rooibos root nodule bacterial communities.
Spectral-power associations reflect amplitude modulation and within-frequency interactions on the sub-second timescale and cross-frequency interactions on the seconds timescale
Authors: Menceloglu Melisa , Grabowecky Marcia , Suzuki Satoru
Published: January 2020

We investigated the global structure of intrinsic cross-frequency dynamics by systematically examining power-based temporal associations among a broad range of oscillation frequencies both within and across EEG-based current sources (sites). We focused on power-based associations that could reveal unique timescale dependence independently of interacting frequencies. Large spectral-power fluctuations across all sites occurred at two characteristic timescales, sub-second and seconds, yielding distinct patterns of cross-frequency associations. On the fast sub-second timescale, within-site (local) associations were consistently between pairs ofβ-γfrequencies differing by a constant Δf(particularly Δf∼ 10 Hz at posterior sites and Δf∼ 16 Hz at lateral sites) suggesting that higher-frequency oscillations are organized into Δfamplitude-modulated packets, whereas cross-site (long-distance) associations were all within-frequency (particularly in the >30 Hz and 6-12 Hz ranges, suggestive of feedforward and feedback interactions). On the slower seconds timescale, within-site (local) associations were characterized by a broad range of frequencies selectively associated with ∼10 Hz at posterior sites and associations among higher (>20 Hz) frequencies at lateral sites, whereas cross-site (long-distance) associations were characterized by a broad range of frequencies at posterior sites selectively associated with ∼10 Hz at other sites, associations among higher (>20 Hz) frequencies among lateral and anterior sites, and prevalent associations at ∼10 Hz. Regardless of timescale, within-site (local) cross-frequency associations were weak at anterior sites indicative of frequency-specific operations. Overall, these results suggest that the fast sub-second-timescale coordination of spectral power is limited to local amplitude modulation and insulated within-frequency long-distance interactions (likely feedforward and feedback interactions), while characteristic patterns of cross-frequency interactions emerge on the slower seconds timescale. The results also suggest that the occipitalαoscillations play a role in organizing higher-frequency oscillations into ∼10 Hz amplitude-modulated packets to communicate with other regions. Functional implications of these timescale-dependent cross-frequency associations await future investigations.
Crystal structure of the giant panda MHC class I complex: first insights into the viral peptide presentation profile in the bear family
Authors: Yuan Hongyu , Ma Lizhen , Zhang Lijie , Li Xiaoying , Xia Chun
Published: January 2020

The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-β2m (aka pMHC-I) trimolecular complex for TCR recognition, which is the critical activation link for triggering antiviral T cell immunity. Ursidae includes 5 genera and 8 species; however, research on T cell immunology in this family, especially structural immunology, is lacking. In this study, the structure of the key trimolecular complex pMHC-1 (aka pAime-128), which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex, including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the panda pMHC-I to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I andβ2m, the features of pAime-128 involved in TCR docking and CD8 binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were concretely clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family.

IMPORTANCE

Ursidae includes 5 genera and 8 species; however, the study of its immunology, especially structural immunology, is extremely rare to date. In this paper, we first crystallized the key complex pMHC-I, taking the giant panda as its representative species. Structural characteristics of the giant panda pMHC-I complexes, contains the unique pockets of PBG were analyzed in detail. Comparison of the panda pMHC-I in the bear family and other mammals, almost definite features was displayed. Meanwhile, the interaction between HC and LV, the unique features of pMHC-I in the CD8 binding and TCR docking, validation of anchor site in the PBG, and epitopes of potential viruses infected with the pandas, were concretely clarified. These unique characteristics of pMHC-I clearly indicate an unusual situation during the evolution of MHC molecules in the endangered pandas. These results also provide a novel platform for further study of panda T cell immunology and vaccines.
New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities
Authors: Baquero Diana P. , Contursi Patrizia , Piochi Monica , Bartolucci Simonetta , Liu Ying , Cvirkaite-Krupovic Virginija , Prangishvili David , Krupovic Mart
Published: January 2020

Viruses of hyperthermophilic archaea represent one of the least understood parts of the virosphere, showing little genomic and morphological similarity to viruses of bacteria or eukaryotes. Here, we investigated virus diversity in the active sulfurous fields of the Campi Flegrei volcano in Pozzuoli, Italy. Virus-like particles displaying eight different morphotypes, including lemon-shaped, droplet-shaped and bottle-shaped virions, were observed and five new archaeal viruses proposed to belong to familiesRudiviridae,GlobuloviridaeandTristromaviridaewere isolated and characterized. Two of these viruses infect neutrophilic hyperthermophiles of the genusPyrobaculum, whereas the remaining three have rod-shaped virions typical of the familyRudiviridaeand infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely,Saccharolobus,AcidianusandMetallosphaera. Notably,Metallosphaerarod-shaped virus 1 is the first rudivirus isolated onMetallosphaeraspecies. Phylogenomic analysis of the newly isolated and previously sequenced rudiviruses revealed a clear biogeographic pattern, with all Italian rudiviruses forming a monophyletic clade, suggesting geographical structuring of virus communities in extreme geothermal environments. Furthermore, we propose a revised classification of theRudiviridaefamily, with establishment of five new genera. Collectively, our results further show that high-temperature continental hydrothermal systems harbor a highly diverse virome and shed light on the evolution of archaeal viruses.
Impact of nanoscale hindrances on the relationship between lipid packing and diffusion in model membranes
Authors: Beckers Daniel , Urbancic Dunja , Sezgin Erdinc
Published: January 2020

Membrane models have allowed for precise study of the plasma membrane’s biophysical properties, helping to unravel both structural and dynamic motifs within cell biology. Free standing and supported bilayer systems are popular models to reconstitute the membrane related processes. Although it is well-known that each have their advantages and limitations, comprehensive comparison of their biophysical properties is still lacking. Here, we compare the diffusion and lipid packing in giant unilamellar vesicles, planar and spherical supported membranes and cell-derived giant plasma membrane vesicles. We apply florescence correlation spectroscopy, spectral imaging and super-resolution STED-FCS to study the diffusivity, lipid packing and nanoscale architecture of these membrane systems, respectively. Our data show that lipid packing and diffusivity is tightly correlated in free-standing bilayers. However, nanoscale interactions in the supported bilayers cause deviation from this correlation. This data is essential to develop accurate theoretical models of the plasma membrane and will serve as a guideline for suitable model selection in future studies to reconstitute biological processes.
Rice NIN-LIKE PROTEIN 4 is a master regulator of nitrogen use efficiency
Authors: Wu Jie , Zhang Zi-Sheng , Xia Jing-Qiu , Alfatih Alamin , Song Ying , Huang Yi-Jie , Wan Guang-Yu , Sun Liang-Qi , Tang Hui , Liu Yang , Wang Shi-Mei , Zhu Qi-Sheng , Qin Peng , Wang Yu-Ping , Li Shi-Gui , Mao Chuan-Zao , Zhang Gui-Quan , Chu Chengcai , Yu Lin-Hui , Xiang Cheng-Bin
Published: January 2020

Nitrogen (N) is one of the key essential macronutrients that affects rice growth and yield. Inorganic N fertilizers are excessively used to boost yield and generate serious collateral environmental pollution. Therefore, improving crop N use efficiency (NUE) is highly desirable and has been a major endeavor in crop improvement. However, only a few regulators have been identified that can be used to improve NUE in rice to date. Here we show that the NIN-like protein OsNLP4 significantly improves the rice NUE and yield. Field trials consistently showed that loss-of-OsNLP4dramatically reduced yield and NUE compared with wild type under different N regimes. In contrast, theOsNLP4overexpression lines remarkably increased yield by 30% and NUE by 47% under moderate N level compared with wild type. Transcriptomic analyses revealed that OsNLP4 orchestrates the expression of a majority of known N uptake, assimilation and signaling genes by directly binding to the nitrate-responsivecis-element in their promoters to regulate their expression. Moreover, overexpression of OsNLP4 can recover the phenotype of Arabidopsisnlp7mutant and enhance its biomass. Our results demonstrate that OsNLP4 is a master regulator of NUE in rice and sheds light on crop NUE improvement.