bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond neutrality: adding habitat filtering to neutral models
Authors: Abeysinghe Wasana , Punchi-Manage Ruwan 
Published: May 2020

AbstractBackgroundUnderstanding the processes that structure species is one of the primary focuses in community ecology. Hubbell’s neutral model shows stochastic processes alone can describe the two macro-ecological patterns, species richness and species-area relationship, of the community. Although Hubbell’s neutral model can explain the macro-ecological patterns of the species at large scales, it paid less attention to construct the spatial structure of the community. Previous studies suggest that such spatial structures are mostly due to habitat filtering processes work at the intermediate spatial scales. Therefore, Hubbell’s neutral model does not explain the full picture of the community structuring due to its fully stochastic nature.ResultsIn this study, we proposed a two-schema model that has the habitat filtering component and the stochastic component to construct the species assemblages seen in the community level. The proposed model uses one additional parameter (i.e. number of individuals in habitat) in addition to Hubbell’s three-parameter neutral model (i.e. fundamental bio-diversity number (θ), dispersal limitation (m) and speciation (v)). The proposed model works at two spatial scales: habitat filtering at the intermediate scales and stochastic processes at the large and very small spatial scales. The model coupled the local community dynamics with the meta-community dynamics. The local community has a fixed area with carrying capacity that is proportional to the local community size. The number of habitats in the proposed model can vary. Individuals are placed into habitats with probabilities according to the habitat suitability. Species richness and species composition in each habitat were calculated. The model is fitted for differentθvalues,mvalues, and a different number of habitats.ConclusionsWe assume that habitat filtering plays an important role together with stochastic processes to structure species in forests. Therefore, the proposed model with only four parameters can explain a large proportion of the species structuring of the communities. We found that more species can be maintained in a heterogeneous environment than a uniform environment. Therefore, habitat conservation is highly important for maintaining species diversity in forest communities.
A simplified LC−MS/MS approach for simultaneous quantification and pharmacokinetics of five compounds in rats following oral administration of Gastrodia elata extract
Authors: Dong Jiajia , Ji De , Su Lianlin , Zhang Fengyang , Tong Huangjin , Mao Chunqin , Lu Tulin 
Published: May 2020

AbstractBackgroundTo support the multicomponent pharmacokinetics ofGastrodia elata, a rapid, simple, and sensitive ultra-performance liquid chromatography tandem with mass spectrometry (LC–MS/MS) approach was established for simultaneous quantification of gastrodin, parishin A, parishin B, parishin C, and parishin E.MethodsFive compounds were extracted from plasma by using one-step protein precipitation. The chromatographic separation was achieved on a C18column with gradient mobile phase comprising acetonitrile and 0.05% formic acid. The detection was performed using negative electrospray ionization in multiple reaction monitoring mode.ResultsThis new method maximizes assay throughput by using minimal sample clean-up procedures and a shorter analytical run time. The approach exhibited good linearity for the five compounds (r2> 0.995) in the concentration ranges. The lower limits of quantification (LLOQ) were determined as 1.37 ng/mL for parishin A, parishin B, parishin C, and parishin E and 10 ng/mL for gastrodin. Then the method was fully validated with intra- and inter-day precision, accuracy, matrix effects, extraction recovery, and stability.ConclusionThis validated approach was successfully applied to the pharmacokinetic study following oral administration ofGastrodia elataextract to rats. This investigation may provide some guidance for the clinical application and explanation of the pharmacological mechanism ofGastrodia elata.
First record of ostracods from the Upper Ordovician red-coloured marine sandstones of the Tierekeawati Formation in Tarim Basin, NW China: implications on palaeoenvironment and palaeobiogeography
Authors: Song Jun-Jun , Shen Yi-Xin , Tang Peng , Zhang Xiao-Le , Li Qi-Jian , Luo Zheng-Jiang 
Published: May 2020

AbstractOstracods are described for the first time from the red-coloured marine sandstones of Arisu section (Arisu red beds) of the Upper Ordovician Tierekeawati Formation in Kalpin area of northwestern Tarim Basin, Xinjiang Uygur Autonomous Region (Xinjiang), Northwest China. Twenty-two species belonging to thirteen genera are described and figured. The ostracod fauna suggests a probable Sandbian–Katian age for these beds. The palaeoecological assemblage of ostracod fauna implies the deposition in a nearshore-offshore environment during a regression when the Arisu red beds of the Tierekeawati Formation were laid down in the Tarim Basin. Many cosmopolitan and provincial genera were present in diversified ostracod fauna of the Arisu red beds, suggesting the possible biogeographic relationships among the Tarim, Tibet, and South China plates, as well as Europe and North America continents during the Late Ordovician. Ostracods experienced faunal exchanges between Laurentia and the Tarim Plate during the Late Ordovician Period.
Transdiagnostic and disease-specific abnormalities in the default-mode network hubs in psychiatric disorders: A meta-analysis of resting-state functional imaging studies
Authors: Doucet Gaelle E. , Janiri Delfina , Howard Rebecca , O’Brien Madeline , Andrews-Hanna Jessica R. , Frangou Sophia 
Published: May 2020

AbstractBackground.The default mode network (DMN) dysfunction has emerged as a consistent biological correlate of multiple psychiatric disorders. Specifically, there is evidence of alterations in DMN cohesiveness in schizophrenia, mood and anxiety disorders. The aim of this study was to synthesize at a fine spatial resolution the intra-network functional connectivity of the DMN in adults diagnosed with schizophrenia, mood and anxiety disorders, capitalizing on powerful meta-analytic tools provided by activation likelihood estimation.Methods.Results from 70 whole-brain resting-state functional magnetic resonance imaging articles published during the last 15 years were included comprising observations from 2,789 patients and 3,002 healthy controls.Results.Specific regional changes in DMN cohesiveness located in the anteromedial and posteromedial cortex emerged as shared and trans-diagnostic brain phenotypes. Disease-specific dysconnectivity was also identified. Unmedicated patients showed more DMN functional alterations, highlighting the importance of interventions targeting the functional integration of the DMN.Conclusion.This study highlights functional alteration in the major hubs of the DMN, suggesting common abnormalities in self-referential mental activity across psychiatric disorders.
Mortality and Advanced Support Requirement for Patients With Cancer With COVID-19: A Mathematical Dynamic Model for Latin America
Authors: Ruiz-Patiño Alejandro , Arrieta Oscar , Pino Luis E. , Rolfo Christian , Ricaurte Luisa , Recondo Gonzalo , Zatarain-Barron Zyanya-Lucia , Corrales Luis , Martín Claudio , Barrón Feliciano , Vargas Carlos , Carranza Hernán , Otero Jorge , Rodriguez July , Sotelo Carolina , Viola Lucia , Russo Alessandro , Rosell Rafael , Cardona Andrés F. 
Published: May 2020

PURPOSEIn the midst of a global pandemic, evidence suggests that similar to other severe respiratory viral infections, patients with cancer are at higher risk of becoming infected by COVID-19 and have a poorer prognosis.METHODSWe have modeled the mortality and the intensive care unit (ICU) requirement for the care of patients with cancer infected with COVID-19 in Latin America. A dynamic multistate Markov model was constructed. Transition probabilities were estimated on the basis of published reports for cumulative probability of complications. Basic reproductive number (R0) values were modeled with R using the EpiEstim package. Estimations of days of ICU requirement and absolute mortality were calculated by imputing number of cumulative cases in the Markov model.RESULTSEstimated median time of ICU requirement was 12.7 days, median time to mortality was 16.3 days after infection, and median time to severe event was 8.1 days. Peak ICU occupancy for patients with cancer was calculated at 16 days after infection. Deterministic sensitivity analysis revealed an interval for mortality between 18.5% and 30.4%. With the actual incidence tendency, Latin America would be expected to lose approximately 111,725 patients with cancer to SARS-CoV-2 (range, 87,116-143,154 patients) by the 60th day since the start of the outbreak. Losses calculated vary between < 1% to 17.6% of all patients with cancer in the region.CONCLUSIONCancer-related cases and deaths attributable to SARS-CoV-2 will put a great strain on health care systems in Latin America. Early implementation of interventions on the basis of data given by disease modeling could mitigate both infections and deaths among patients with cancer.
Variability in Cytogenetic Testing for Multiple Myeloma: A Comprehensive Analysis From Across the United States
Authors: Yu Yang , Brown Wade Niquelle , Hwang Amie E. , Nooka Ajay K. , Fiala Mark A. , Mohrbacher Ann , Peters Edward S. , Pawlish Karen , Bock Cathryn , Van Den Berg David J. , Rand Kristin A. , Stram Daniel , Conti David V. , Auclair Daniel , Colditz Graham A. , Mehta Jayesh , Haiman Christopher A. , Terebelo Howard , Janakiraman Nalini , Singhal Seema , Chiu Brian , Vij Ravi , Bernal-Mizrachi Leon , Zonder Jeffrey A. , Huff Carol A. , Lonial Sagar , Orlowski Robert Z. , Cozen Wendy , Ailawadhi Sikander 
Published: May 2020

Purpose: Multiple myeloma (MM) treatment has changed tremendously, with significant improvement in patient out-comes. One group with a suboptimal benefit is patients with high-risk cytogenetics, as tested by conventional karyotyping or fluorescence in situ hybridization (FISH). Methodology for these tests has been published, but not necessarily standardized. Methods: We address variability in the testing and reporting methodology for MM cytogenetics in the United States using the ongoing African American Multiple Myeloma Study (AAMMS). We evaluated clinical and cytogenetic data from 1,221 patients (1,161 with conventional karyotyping and 976 with FISH) tested between 1998 and 2016 across 58 laboratories nationwide. Results: Interlab and intralab variability was noted for the number of cells analyzed for karyotyping, with a significantly higher number of cells analyzed in patients in whom cytogenetics were normal (P 5.0025). For FISH testing, CD138-positive cell enrichment was used in 29.7% of patients and no enrichment in 50% of patients, whereas the remainder had unknown status. A significantly smaller number of cells was analyzed for patients in which CD138 cell enrichment was used compared with those without such enrichment (median, 50 v 200; P, .0001). A median of 7 loci probes (range, 1-16) were used for FISH testing across all laboratories, with variability in the loci probed even within a given laboratory. Chromosome 13–related abnormalities were the most frequently tested abnormality (n5956; 97.9%), and t(14;16) was the least frequently tested abnormality (n 5 119; 12.2%). Conclusions: We report significant variability in cytogenetic testing across the United States for MM, potentially leading to variability in risk stratification, with possible clinical implications and personalized treatment approaches.
InSight Care Pilot Program: Redefining Seeing a Patient
Authors: Daly Bobby , Kuperman Gilad , Zervoudakis Alice , Baldwin Medsker Abigail , Roy Ankita , Ro Alice S. , Arenas Javiera , Yanamandala Hrudaya Veena , Kottamasu Raj , Salvaggio Rori , Holland Jessie , Hirsch Stephanie , Walters Chasity B , Lauria Tara , Chow Kim , Begue Aaron , Rozenshteyn Margarita , Zablocki Melissa , Dhami Amandeep K. , Silva Nicholas , Brown Emily , Katzen Lauren L. , Chiu Yeneat O. , Perry Claire , Sokolowski Stefania , Wagner Isaac , Veach Stephen R. , Grisham Rachel N. , Dang Chau T. , Reidy-Lagunes Diane L. , Simon Brett A. , Perchick Wendy 
Published: May 2020

PURPOSE: Early detection and management of symptoms in patients with cancer improves outcomes. However, the optimal approach to symptom monitoring and management is unknown. InSight Care is a mobile health intervention that captures symptom data and facilitates patient-provider communication to mitigate symptom escalation. PATIENTS AND METHODS: Patients initiating antineoplastic treatment at a Memorial Sloan Kettering regional location were eligible. Technology supporting the program included the following: a predictive model that identified patient risk for a potentially preventable acute care visit; a secure patient portal enabling communication, televisits, and daily delivery of patient symptom assessments; alerts for concerning symptoms; and a symptom-trending application. The main outcomes of the pilot were feasibility and acceptability evaluated through enrollment and response rates and symptom alerts, and perceived value evaluated on the basis of qualitative patient and provider interviews. RESULTS: The pilot program enrolled 100 high-risk patients with solid tumors and lymphoma (29% of new treatment starts v goal of 25%). Over 6 months of follow-up, the daily symptom assessment response rate was 56% (the goal was 50%), and 93% of patients generated a severe symptom alert. Patients and providers perceived value in the program, and archetypes were developed for program improvement. Enrolled patients were less likely to use acute care than were other high-risk patients. CONCLUSION: InSight Care was feasible and holds the potential to improve patient care and decrease facility-based care. Future work should focus on optimizing the cadence of patient assessments, the workforce supporting remote symptom management, and the return of symptom data to patients and clinical teams.
Mixed Response to Immunotherapy in Patients with Metastatic Melanoma
Authors: Rauwerdink Daan Jan Willem , Molina George , Frederick Dennie Tompers , Sharova Tanya , van der Hage Jos , Cohen Sonia , Boland Genevieve Marie 
Published: May 2020

AbstractBackgroundImmunotherapy has improved overall survival in metastatic melanoma. Response to therapy can be difficult to evaluate as the traditionally used RECIST 1.1 criteria do not capture heterogeneous responses. Here we describe the clinical characterization of melanoma patients with a clinically defined mixed response to immunotherapy.MethodsThis was a single institution, retrospective analysis of stage IV melanoma patients who received first-line anti-CTLA-4, anti-PD1, or combination anti-CTLA-4/anti-PD1. Therapy response was assessed via clinical definitions, which consisted of cross-sectional imaging combined with clinical exam. Course of disease, clinicopathological characteristics, and management in patients with a mixed clinical response were analyzed.ResultsIn 292 patients (anti-CTLA4 = 63; anti-PD1 = 148, anti-CTLA4/anti-PD1 = 81), 103 were responders (35%), 64 mixed responders (22%), and 125 patients had progressive disease (43%). Of patients with a mixed response, 56% eventually had response to therapy (mixed response followed by response, MR–R), while 31% progressed on therapy (MR–NR). MR–NR patients had higher median LDH (p < 0.01), 3 or more organ sites with metastases (p < 0.01), and more frequently had M1d disease (p < 0.01). Mixed responders who underwent surgery (n = 20) had a significantly longer mean OS compared to patients who did not undergo surgery (6.9 years, 95% CI 6.2–7.6 vs. 6.0 years, 95% CI 4.6–7.3,p = 0.02).DiscussionMixed response to immunotherapy in metastatic melanoma was not uncommon in our cohort (22%). Clinical characteristics associated with progression of disease after initial mixed response included higher LDH, brain metastases, and ≥ 3 organ sites with metastases. Surgical treatment for highly selected patients with a mixed response was associated with improved outcomes.
Optimization of bioremediation-cocktail for application in the eco-recovery of crude oil polluted soil
Authors: Agbaji Joseph E. , Nwaichi Eucharia O. , Abu Gideon O. 
Published: May 2020

Background: Environmental sustainability is the driver for finding the optimal bioremediation cocktail with the combination of highly potent hydrocarbonoclastic strains and the nutrient additives that significantly enhance mineralization of crude oil in polluted soil in order to mitigate its deleterious effects on the environment. In this study, four hydrocarbon-degrading bacterial strains were pre-selected from mined rhizobacterial isolates in aged crude oil-contaminated soil. Method: Agrowaste residues of poultry-droppings, corn chaff, and plantain peel were selected among others for their ability to support high biomass of selected bacterial strains. Baseline proximate analysis was performed on the agrowaste residues. Simplified, one variable at a time (OVAT) was employed in the validation of the variables for optimization using the Multivariate analysis tool of Response Surface Methodology (RSM). To test the significant formulation variables, the Box-Behnken approach using 15 runs design was adopted. Results: The rate of contaminant removal was observed to fit into a quadratic function. For optimal rate or contaminant removal, the fitted model predicted the optimal formulation cocktail condition to be within 0.54 mg/kg (Corn steep liquor), phosphate 137.49 mg/kg (poultry droppings) and 6.4% inocula for initial TPH of 9744 mg kg-1 and THC of 9641 mg kg-1 contaminant level. The model for the application of the bioremediation product and the variables evaluated had a significant p-value < 0.005 for the attainment of 85 to 96 % of TPH and THC removal after 56 days of treatment. Conclusions: This study has shown the need to harness the abundant agrowaste nutrients in supporting high throughput rhizobacteria in the formulation of a bioremediation agent suitable for use in the reclamation of oil spill sites in the Niger Delta oil-producing region.
High linearity silicon modulator capable of actively compensating input distortion
Authors: Zhang Qiang , Yu Hui , Xia Penghui , Fu Zhilei , Wang Xiaofei , Yang Jianyi 
Published: May 2020

In this Letter, we demonstrate an ultra-high linearity silicon carrier-depletion-based modulator by integrating a dual-parallel Mach–Zehnder modulator (DP-MZM) with a

1

×

2

thermo-optical switch. The operation principle is to manipulate power distributions of RF and optical signals among the two sub-MZMs, so their third-order nonlinearities can cancel each other. Spurious-free dynamic ranges (SFDRs) for the third-order intermodulation distortion (IMD3) are measured to be

123

/

120

d
B
⋅
H

z

6

/

7

at 1/10 GHz, which represents a record-high linearity achieved with silicon-based modulators. As a contrast, SFDRs of a reference single MZM are

113

/

108

d
B
⋅
H

z

4

/

5

at the same frequencies. Furthermore, we first demonstrate that this device is able to actively compensate nonlinear distortions of RF driving signals in the optical domain. Carrier-to-distortion ratios (CDRs) of deliberately distorted two-tone signals are improved from 40/50 dB to 45/72 dB after the modulation.
Ultra-compact silicon mode-order converters based on dielectric slots
Authors: Zhao Yaotian , Guo Xuhan , Zhang Yong , Xiang Jinlong , Wang Kangnian , Wang Hongwei , Su Yikai 
Published: May 2020

Ultra-compact mode-order converters with dielectric slots are demonstrated on a silicon-on-insulator platform. We propose a mode converter that converts the TE0 mode into the TE1 mode with an ultra-small footprint of only

0.8

×

1.2

µ

m

2

. The measured insertion loss is less than 1.2 dB from 1520 nm to 1570 nm. To reduce the insertion loss, we further optimize the structure and design two mode converters that convert the TE0 mode into the TE1 mode and the TE2 mode with footprints of

0.88

×

2.3

µ

m

2

and

1.4

×

2.4

µ

m

2

, respectively. Their measured insertion losses are both less than 0.5 dB. Additionally, the proposed devices are cascadable and scalable for high-order mode conversion.
Ultra-low NA step-index large mode area Yb-doped fiber with a germanium doped cladding for high power pulse amplification
Authors: Sidharthan Raghuraman , Lin Di , Jie Lim Kang , Li Huizi , Huiting Lim Serene , Jian Chang Chen , Men Seng Yue , Liang Chua Song , Jung Yongmin , Richardson David J. , Yoo Seongwoo 
Published: May 2020

High concentration rare earth doped, large mode area (LMA) step-index fibers, which feature a very high cladding absorption per unit length at the pump wavelength, high efficiency, and excellent beam quality, are ideal for high power pulsed fiber lasers/amplifiers where large effective mode areas and short device lengths are crucial in order to reduce detrimental nonlinear effects associated with high peak power operation. In this Letter, we realize low numerical aperture (NA) high absorption fibers, simply by employing a germanium (Ge)-doped cladding rather than a pure silica cladding to offset the high refractive index associated with using a high concentration of ytterbium (Yb) in the core. This approach allows us to separate the two inter-linked fiber design parameters of pump absorption and NA in a step-index fiber. Using a conventional modified chemical vapor deposition process combined with solution doping, a low NA (0.04), LMA (

475

µ

m

2

) silica fiber is fabricated with a cladding absorption value of

>

20

d
B

/

m

, which is the highest value among LMA step-index fibers with

N
A

<
0.06

so far reported to the best of our knowledge. The fabricated Yb-doped fiber was tested in a high-power picosecond amplifier system and enabled the generation of 190 ps laser pulses with a 101 µJ pulse energy and 0.5 MW peak power at an average power of 150 W.
Tunable Fano-like resonances in bent single-mode waveguide-based Fabry–Perot resonator: erratum
Authors: Dyshlyuk Anton V. 
Published: May 2020

In this erratum, we correct an error in the numerical simulation
results published in Opt. Lett. 44, 231
(2019)OPLEDP0146-959210.1364/OL.44.000231. The error arose from
disregarding cladding modes in the straight input and output waveguide
sections [Fig. 2(a) in the original paper]. Although these modes do
not contribute directly to the calculated power in the reflected and
transmitted fundamental modes in those sections, they do,
nevertheless, play a significant role in shaping the reflection and
transmission spectra of the bent resonator, as was found after the
paper had been published. While the main findings of the original
paper remain largely intact, quantitatively the spectra in Figs. 3–6
are inaccurate and must be replaced with the correct ones given in
this erratum. Some minor modifications to the conclusions of the
original paper that are required in view of the corrected results are
also discussed.