bluuebunny/crossref_metadata_2025_split huggingface dataset:
FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
Authors: Hennion Magali , Arbona Jean-Michel , Lacroix Laurent , Cruaud Corinne , Theulot Bertrand , Tallec Benoît Le , Proux Florence , Wu Xia , Novikova Elizaveta , Engelen Stefan , Lemainque Arnaud , Audit Benjamin , Hyrien Olivier 
Published: May 2020

AbstractGenome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates from Saccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4964 and 4485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.
Catamenial rectal bleeding due to invasive endometriosis: a case report
Authors: Keith Joshua J. , Hernandez Lorenzo O. , Maruoka Nishi Livia Y. , Jethwa Tarang P. , Lewis Jason T. , Pujalte George G. A. 
Published: May 2020

Abstract
Background
Although gastrointestinal involvement is the most common site for extra-genital endometriosis, deep infiltrative endometriosis, which affects the mucosal layer, is very rare.

Case presentation
We present a case of a 41-year-old white woman with cyclic rectal bleeding. Magnetic resonance imaging was done, together with colonoscopy and histologic staining of biopsied samples, which led to the final diagnosis of intestinal invasive endometriosis with recto-sigmoid stricture. Our patient was treated symptomatically with stool softeners.

Conclusion
This case provides a rare example of catamenial bleeding. It is important to keep invasive endometriosis on the differential diagnosis whenever a premenopausal woman has cyclical rectal bleeding.
Quantifying the role of social distancing, personal protection and case detection in mitigating COVID-19 outbreak in Ontario, Canada
Authors: Wu Jianhong , Tang Biao , Bragazzi Nicola Luigi , Nah Kyeongah , McCarthy Zachary 
Published: May 2020

AbstractPublic health interventions have been implemented to mitigate the spread of coronavirus disease 2019 (COVID-19) in Ontario, Canada; however, the quantification of their effectiveness remains to be done and is important to determine if some of the social distancing measures can be relaxed without resulting in a second wave. We aim to equip local public health decision- and policy-makers with mathematical model-based quantification of implemented public health measures and estimation of the trend of COVID-19 in Ontario to inform future actions in terms of outbreak control and de-escalation of social distancing. Our estimates confirm that (1) social distancing measures have helped mitigate transmission by reducing daily infection contact rate, but the disease transmission probability per contact remains as high as 0.145 and case detection rate was so low that the effective reproduction number remained higher than the threshold for disease control until the closure of non-essential business in the Province; (2) improvement in case detection rate and closure of non-essential business had resulted in further reduction of the effective control number to under the threshold. We predict the number of confirmed cases according to different control efficacies including a combination of reducing further contact rates and transmission probability per contact. We show that improved case detection rate plays a decisive role to reduce the effective reproduction number, and there is still much room in terms of improving personal protection measures to compensate for the strict social distancing measures.
Assessing the wood sourcing practices of the U.S. industrial wood pellet industry supplying European energy demand
Authors: Kittler Brian , Stupak Inge , Smith C. Tattersall 
Published: May 2020

Abstract
Background
As the demand for wood pellets has increased in EU member states, so has a multi-pronged examination of the environmental effects of establishing a transatlantic trade in wood pellets between the U.S. and Europe. However, the nature of industrial wood pellet supply chains is poorly understood or little known. This work aimed to understand the feedstock sourcing strategies being used by the wood pellet industry in the southeast U.S., commonly applied approaches to documenting sustainability of these feedstocks, and drivers operating behind related developments.

Methods
This study used structured interviews of sustainability managers and procurement staff at pellet mills comprising 75% of the U.S. industrial pellet sector. The industry was classified into types of supply chains, based on the role of loggers, wood dealers, sawmills, and other wood product facilities in the supply chains. Additional classifications examined feedstock types and origins, number and type of suppliers, contractual relationships with suppliers, applied procurement systems, risk assessment and due-diligence methodologies, risk mitigation procedures, and supply chain certifications.

Results
Three main types of supply chains were identified within the U.S. industrial pellet sector, differentiated based on features of feedstock procurement, risk assessment procedures, and risk management. The study observed a slight shift toward using a higher proportion of wood residuals as feedstock in some of the larger pellet mills. Policy requirements, customer orders, and external pressures were driving the sector’s adoption of sustainability programs, with risk assessments and wood procurement procedures aligned to policy requirements.

Conclusions
The strength of a risk-based approach to sustainability documentation depends on the quality of source data on risks within a sourcing area, scale of analysis, and integration of risk assessments into procurement practices. Some risk categories are more difficult to assess and control. Challenges increase with increasing number and diversity of supply chain actors and depend on the nature of agreements between these entities for the conveyance of feedstocks to pellet mills. Fiber procurement is similar to pulpwood-using industries, but extending the risk assessment to residuals is complicated and challenging to the sector. The study identified a number of strategies in use within pellet mill supply chains for dealing with these challenges.
Optimization of pH as a strategy to improve enzymatic saccharification of wheat straw for enhancing bioethanol production
Authors: Abdulsattar M. O. , Abdulsattar J. O. , Greenway G. M. , Welham K. J. , Zein S. H. 
Published: May 2020

AbstractIn this work, wheat straw (WS) was used as a lignocellulosic substrate to investigate the influence of pH on enzymatic saccharification. The optimum enzymatic hydrolysis occurred at pH range 5.8–6.0, instead of 4.8–5.0 as has been widely reported in research. Two enzymes cocktails, Celluclast® 1.5 L with Novozymes 188, Cellic® CTec2 and endo-1,4-β-xylanase, were used for the pH investigation over a pH range of 3.0–7.0. The highest concentration of total reduced sugar was found at pH 6.0 for all the different enzymes used in this study. The total reduced sugar produced from the enzymatic saccharification at pH 6.0 was found to be 7.0, 7.4, and 10.8 (g L−1) for Celluclast® 1.5 L with Novozymes 188, endo-1,4-β-xylanase and Cellic® CTec2, respectively. By increasing the pH from 4.8 to 6.0, the total reduced sugar yield increased by 25% for Celluclast® 1.5 L with Novozymes 188 and endo-1 4-β-xylanase and 21% for Cellic® CTec2. The results from this study indicate that WS hydrolysis can be improved significantly by elevating the pH at which the reaction occurs to the range of 5.8 to 6.0.
Approving the biocontrol method of potato wilt caused by Ralstonia solanacearum (Smith) using Enterobacter cloacae PS14 and Trichoderma asperellum T34
Authors: Mohamed Bereika F. F. , Sallam Nashwa M. A. , Alamri Saad A. M. , Abo-Elyousr Kamal A. M. , Mostafa Yasser S. , Hashem Mohamed 
Published: May 2020

AbstractThis study aimed to evaluate the efficiency ofEnterobacter cloacaePS14 andTrichoderma asperellumT34 in the control of potato wilt, caused byRalstonia solanacearum(Smith), under greenhouse and field conditions. In vitro, the endophyteE.cloacaePS14 caused the highest reduction of the pathogen growth among 7 screened bacteria. It produced an inhibition zone as 16.9 mm compared to a specific antibiotic (20.0 mm).E.cloacaePS14 was selected as an effective antagonistic bacterium to be compared toT.asperellumstrain T34 for reduction of the disease as well as increasing the crop yield of potato plants. BothE.cloacaeandT.asperellumreduced the disease severity up to 10.7–26.5%, respectively, under greenhouse and up to 26.6–36.6%, respectively, under field conditions. The results approved that bothE.cloacaeandT.asperellumincreased the yield of the crop by 20.44–40.96%, respectively. Their mode of action was indicated by suppression of the pathogen as well as induction of plant systemic resistance. The induction of systemic resistance was confirmed by increasing the total phenol and salicylic acid contents as well as increasing the activities of peroxidase, lipoxygenase, and polyphenol oxidase in potato plants than the healthy or only infected plants. Production of siderophore, indole-3-acetic acid (0.577–0.884 μM), hydrogen cyanide (2.34–3.61 μg/ml), and salicylic acid (0.436–1.488 μg/ml) was confirmed by E. cloacae PS14 andT.asperellumT34, respectively, in vitro. The study recommends the new strainE.cloacaePS14, as new endophytic effective bacteria, in the control ofR.solanacearumcausing the potato wilt disease.
Multicenter Study of Risk-Adapted Therapy With Dose-Adjusted EPOCH-R in Adults With Untreated Burkitt Lymphoma
Authors: Roschewski Mark , Dunleavy Kieron , Abramson Jeremy S. , Powell Bayard L. , Link Brian K. , Patel Prapti , Bierman Philip J. , Jagadeesh Deepa , Mitsuyasu Ronald T. , Peace David , Watson Peter R. , Hanna Wahid T. , Melani Christopher , Lucas Andrea N. , Steinberg Seth M. , Pittaluga Stefania , Jaffe Elaine S. , Friedberg Jonathan W. , Kahl Brad S. , Little Richard F. , Bartlett Nancy L. , Fanale Michelle A. , Noy Ariela , Wilson Wyndham H. 
Published: May 2020

PURPOSE Burkitt lymphoma is an aggressive B-cell lymphoma curable with dose-intensive chemotherapy derived from pediatric leukemia regimens. Treatment is acutely toxic with late sequelae. We hypothesized that dose-adjusted etoposide, doxorubicin, cyclophosphamide, vincristine, prednisone, and rituximab (DA-EPOCH-R) may obviate the need for highly dose-intensive chemotherapy in adults with Burkitt lymphoma. METHODS We conducted a multicenter risk-adapted study of DA-EPOCH-R in untreated adult Burkitt lymphoma. Low-risk patients received three cycles without CNS prophylaxis, and high-risk patients received six cycles with intrathecal CNS prophylaxis or extended intrathecal treatment if leptomeninges were involved. The primary endpoint was event-free survival (EFS), and secondary endpoints were toxicity and predictors of EFS and overall survival (OS). RESULTS Between 2010 and 2017, 113 patients were enrolled across 22 centers, and 98 (87%) were high risk. The median age was 49 (range, 18-86) years, and 62% were ≥ 40 years. Bone marrow and/or CSF was involved in 29 (26%) of patients, and 28 (25%) were HIV positive. At a median follow-up of 58.7 months, EFS and OS were 84.5% and 87.0%, respectively, and EFS was 100% and 82.1% in low- and high-risk patients. Therapy was equally effective across age groups, HIV status, and International Prognostic Index risk groups. Involvement of the CSF identified the group at greatest risk for early toxicity-related death or treatment failure. Five treatment-related deaths (4%) occurred during therapy. Febrile neutropenia occurred in 16% of cycles, and tumor lysis syndrome was rare. CONCLUSION Risk-adapted DA-EPOCH-R therapy is effective in adult Burkitt lymphoma regardless of age or HIV status and was well tolerated. Improved therapeutic strategies for adults with CSF involvement are needed (funded by the National Cancer Institute; ClinicalTrials.gov identifier: NCT01092182 ).
Examination of the needs of hygienizational patients of periodontological guidelines in Lublin
Authors: Baranowski Mateusz , Wójcicka Agnieszka , Czerniakiewicz Kacper , Wysokińska-Miszczuk Joanna 
Published: May 2020

Introduction: The dental treatment of every patient, who comes to the dental office, should start with his hygienization. The basis of treatment should be daily, careful oral hygiene at home. Clinical observations suggest that patients neglect or perform this incorrectly. Purpose of work: The aim of the study was to assess the oral hygiene condition of patients reporting to the periodontics clinic Materials and Methods: The medical documentation of 52 patients who came to the Clinic of Periodontology at the Clinical Center of the Medical University in Lublin in 2015-2016 was analyzed. There were 24 men and 28 women between 19 and 75 years of age. Extraoral and intraoral examination were performed and general medical history was taken. The CPITN index was used to assess the presence of dental deposits and tartar. Results: In the group of respondents; 47 patients [90.38%] required professional hygienization. Conclusions: Although almost all patients declare meticulous removal of dental deposits at least twice a day, more than 90% have shown numerous abnormalities in brushing or irregular oral hygiene. Patients do not have the skills or neglect to maintain oral hygiene, while being convinced about compliance with the hygiene regime. The doctor's role is to create conditions for education and patient motivation
Development of dysbiosis in the organism of rats receiving a high-fat diet
Authors: Levitsky A. P. , Markov A. V. , Pupin T. I. 
Published: May 2020

Background. To determine the effect on the degree of dysbiosis in the organs and tissues of rats treated with high-fat diet (HFD) using fats with various fatty acid compositions.Methods. We used ordinary (high-linoleic) sunflower oil, high-oleic sunflower oil, butter, palm and coconut oils. Rats were fed with 15 % of each of the fats for 64 days. In the blood serum from v.cava and v. porta, in the liver, heart, brain, skeletal muscles and intestinal mucosa, urease activity (an indicator of bacterial insemination), lysozyme activity (a factor of non-specific immunity) were determined, and the degree of dysbiosis was calculated from the ratio of relative urease and lysozyme activities. Results. The activity of urease in the blood of v. porta increased in rats treated with HFD, and was significantly higher than in the blood of v.cava. In most of the studied tissues, urease activity increased after HFD, with the exception of rats receiving high-oleic sunflower oil (HOSO). In contrast, lysozyme activity was reduced in most tissues, with the exception of rats treated with HOSO. The degree of dysbiosis increased after HFD with the exception of rats treated with HOSO.Conclusion. HFD increases the translocation of bacteria from the intestine. The liver partially neutralizes the microflora coming from the intestines. In blood serum from v. cava and v. porta, urease activity (an indicator of bacterial contamination), lysozyme activity (nonspecific immunity factor) were determined in the liver, heart, brain, skeletal muscle and intestinal mucosa, and the degree of dysbiosis was calculated by the ratio of the relative activities of urease and lysozyme.Results. Blood urease activity v. porta was elevated in rats treated with HFD and was significantly higher than in blood v. cava. In most of the tissues studied, urease activity increased after HFD with the exception of rats treated with high oleic sunflower oil (HOSO), the development of dysbiosis in all tissues of the body. The exception is HOSO, which does not cause the development of dysbiosis and inflammation.
Optomechanical inertial sensors
Authors: Hines Adam , Richardson Logan , Wisniewski Hayden , Guzman Felipe 
Published: May 2020

We present a performance analysis of compact monolithic optomechanical inertial sensors that describes their key fundamental limits and overall acceleration noise floor. Performance simulations for low-frequency gravity-sensitive inertial sensors show attainable acceleration noise floors on the order of

1
×

10

−
11

m

/

s

2

H
z

. Furthermore, from our performance models, we devised an optimization approach for our sensor designs, sensitivity, and bandwidth trade space. We conducted characterization measurements of these compact mechanical resonators, demonstrating

mQ

-products at levels of 250 kg, which highlight their exquisite acceleration sensitivity.
Iron-based metallic glass for improved resolution, maskless phase-change photolithography
Authors: He Chao , Yang Zhe , Chen Chao , Tong Hao , Miao Xiangshui 
Published: May 2020

Phase-change lithography (PCL) is expected to become the next generation of mainstream lithography for its high efficiency, non-toxic nature, and maskless technique. However, the low resolution of current PCL limits its practical application. We propose to use FeMoCrCBY metallic glass film as a high-resolution photoresistor in PCL, which can greatly improve the resolution more than other metallic glasses because of its high heat capacity and crystallization temperature. Thermal distribution in FeMoCrCBY indicates that the feature size of the phase transition region can controllably be made smaller. For example, the size of micro-patterns observed by scanning electron microscope (SEM) is around 1.3 µm. The resolution can be further improved by reducing the laser spot size. Our results show that metallic glass film FeMoCrCBY is a promising photoresistor for high-resolution PCL.
Ultracompact optical fiber acoustic sensors based on a fiber-top spirally-suspended optomechanical microresonator
Authors: Yao Mian , Zhang Yangxi , Ouyang Xia , Ping Zhang A. , Tam Hwa-Yaw , Wai P. K. A. 
Published: May 2020

Acoustic wave sensors with a high sensitivity and small size are highly desired for a wide variety of important and emerging applications such as photoacoustic gas sensing and bio-imaging. Here we present an ultracompact optical fiber acoustic sensor based on an optomechanical resonator that is directly in situ printed on the end face of a standard single-mode optical fiber by using an optical 3D μ-printing technology. The fiber-top optomechanical microresonator is composed of a microscale suspended polymer micro-disk that forms a Fabry–Perot interferometric cavity, together with the optical fiber end face, and acts as the acoustic wave-sensitive micromechanical resonator simultaneously. The microbeams for suspending the micro-disk are devised with a spiral structure to overcome the small-size imposed low deflection amplitude so as to improve its sensitivity to acoustic waves. The sensor with a high sensitivity of 118.3 mV/Pa and low noise equivalent acoustic signal level of

0.328

µ

P
a

/

H
z

1

/

2

at audio frequency is experimentally demonstrated. Moreover, with a resonance amplification mechanism, the sensitivity can be enhanced by 40.1 times when the frequency of the acoustic wave matches with the natural resonance frequency of the optomechanical resonator. Such an ultrasmall fiber-tip acoustic sensor has not only a miniaturization-induced broad bandwidth, but also a structure-enhanced ultrahigh sensitivity and thus is very promising in various acoustic wave-based sensing, imaging, and testing applications.
Sub-megahertz linewidth 780.24  nm distributed feedback laser for87Rb applications
Authors: Di Gaetano E. , Watson S. , McBrearty E. , Sorel M. , Paul D. J. 
Published: May 2020

A distributed feedback GaAs-based semiconductor laser with a laterally coupled grating is demonstrated at a wavelength of 780.24 nm with up to 60 mW power. A mode expander and aluminum-free active layers have been used to reduce the linewidth to 612 kHz while maintaining high output power. The laser demonstrates over 40 dB side-mode suppression ratio with>0.3nmof tuning suitable for atom cooling experiments with the D287Rbatomic transition. This laser has substantial potential to be integrated into miniaturized cold atom systems.
Repeated Occurrences of Basal Cell Cancer in Patients With Inflammatory Bowel Disease Treated With Immunosuppressive Medications
Authors: Khan Nabeel , Patel Dhruvan , Trivedi Chinmay , Kavani Himanshu , Medvedeva Elina , Pernes Tyler , Xie Dawei , Lewis James , Yang Yu-Xiao 
Published: May 2020

INTRODUCTION:
There are limited data on repeated basal cell cancer (BCC) occurrences among patients with inflammatory bowel disease (IBD), especially the impact of continuing immunosuppressive medications.

METHODS:
We conducted a retrospective cohort study of 54,919 patients with IBD followed in the Veterans Affairs Healthcare System. We identified patients who had an incident BCC after their IBD diagnosis. We defined patients' exposure based on their IBD medications use as follows: (i) only aminosalicylate (5-ASA) use, (ii) only active thiopurine (TP) use, (iii) past TP use (discontinued >6 months ago) and no antitumor necrosis factor (TNF) use, (iv) anti-TNF use after previous TP use, (v) only anti-TNF use, and (vi) active anti-TNF and TP use. The outcome of interest was the repeated occurrence of BCC. Adjusted and unadjusted hazard ratios with 95% confidence intervals were used to estimate the risk of repeated BCC occurrence.

RESULTS:
A total of 518 patients developed BCC after their IBD diagnosis. The numbers of repeated BCC occurrences per 100 person-years were 12.8 (5-ASA use only), 34.5 (active TP use), 19.3 (past TP use and no anti-TNF use), 25.4 (anti-TNF use after previous TP use), 17.8 (only anti-TNF use), and 22.4 (active anti-TNF and TP use). Compared with 5-ASA use alone, only active TP use was associated with an increased risk for repeated BCC occurrence (adjusted hazard ratio 1.65, 95% confidence interval 1.24–2.19; P = 0.0005). However, the increased risk was no longer present for other exposure categories.

DISCUSSION:
Among IBD patients who developed an incident BCC while taking a TP and continued it, there was an increased risk of repeated BCC occurrences.
The Impact of International Trade on Environmental Quality: Implications for Law
Authors: Pham Ngoc-Tham , Pham Trung-Kien , Cao Viet Hieu , Tran Ha Giang , Vo Xuan Vinh 
Published: May 2020

Abstract
Our study illuminates the impact of international trade on environmental quality in lower-middle-income countries by using CO2 emission as the proxy for environmental degradation. Using the Pooled Mean Group estimation along with validity tests, the results show that in the long run, CO2 emission is affected by merchandise export, merchandise import, FDI, GDP per capita, and renewable energy consumption. The impact of trade on CO2 emission is mixed because our findings show that merchandise export and import have opposite effects. In addition, our results reveal that Environmental Kuznets Curve exists in the long run with N-sharped. The increase in GDP per capita leads to the raise of CO2 emission at first, but later comes the decrease and then increase. The paper has relevant implications for law makers.
Positivity and monotonicity results for triple sequential fractional differences via convolution
Authors: Goodrich Christopher S. , Lyons Benjamin 
Published: May 2020

AbstractWe investigate the relationship between the discrete fractional difference(\Delta^{\gamma}\circ\Delta^{\beta}\circ\Delta^{\alpha}f)(t)and the positivity or monotonicity of the functionf. Our approach relies on interpreting the fractional difference as an appropriate convolution operator. The results we provide demonstrate that when compared to the double sequential case, i.e.,{(\Delta^{\beta}\circ\Delta^{\alpha}f)(t)}, there is relatively more complexity observed.