bluuebunny/crossref_metadata_2025_split huggingface dataset:
An efficient CRISPR/Cas9 system for simultaneous editing two target sites in Fortunella hindsii
Authors: Xu Yanhui , Zhang Li , Lu Liqing , Liu Jihong , Yi Hualin , Wu Juxun 
Published: March 2022

Abstract
The CRISPR/Cas9 system is a revolutionary genome editing technique and has been widely used in numerous plants. For plants (e.g. citrus) with very low transformation efficiency, how to optimize gene editing efficiency and induce large-fragment deletion has been the focus of research. Here, we report that CRISPR/Cas9 induces efficient deletion of 16–673 bp fragments in the genome of Fortunella hindsii. The ability of two binary vectors, pK7WG2D and pMDC32, to introduce specific mutations into the genome of F. hindsii was evaluated. Double single guide RNAs (sgRNAs) were designed to achieve precise editing of two sites of a gene and deletion of fragments between the two sites. The construction of vectors based on Golden Gate assembly and Gateway recombination cloning is simple and efficient. pK7WG2D is more suitable for F. hindsii genome editing than the pMDC32 vector. Editing efficiency using the pK7WG2D vector reached 66.7%. Allele mutation frequency was 7.14–100%. Plants with 100% allele mutations accounted for 39.4% (13 100% allele mutation plants/33 mutants). The proportion of mutant plants with fragment deletion induced by this editing system was as high as 52.6% (10 fragment-deletion mutants/19 FhNZZ mutants). Altogether, these data suggest that our CRISPR/Cas9 platform is capable of targeted genome editing in citrus and has broad application in research on the citrus functional genome and citrus molecular breeding.
Apple, Test of Insecticides, 1976
Authors: Asquith Dean , Hull Larry A. , Travis James W. , Mowery Paul D. 
Published: March 2022

Abstract
Experimental sprays were applied to run-off to single-tree plots in a complete randomized block design with 4 replicates of Golden Delicious except GCP-5126 which was applied to 4 York Imperial trees, a better host of the white apple leafhopper. Treated single-frees were separated by others not sprayed with insecticides. Experimental sprays were applied with a John Bean sprayer, 35 gpm pump, equipped with a spray mast carrying 7 spray guns arranged to wet the uniformly trimmed trees. Spray dates for the test insecticides were: Apr 27, May 7, Aug 3 and Aug 18 only for GCP-5126. Guthion was applied to these same trees on May 25, June 8 and June 23. Other test insecticides were applied on May 6 and 7, May 25, June 8, June 23, Aug 3 and 4, and Aug 18 and 19. The split dates indicate interruption of spraying by weather. Both dosages of Sumithion were discontinued after June 23. During May, general sprays involving Cyprex, Polyram, sulfur, and calcium chloride were applied as 6X concentrates with an airblast sprayer to the whole experimental block. From June 1 to July 6, the general sprays involved captan, sulfur, and calcium chloride. Late season general sprays were of captan and zineb. Average temperatures weTe: May 57.74° F, June 71.30° F, July 70.09° F, August 67.92° F, and September 62.78° F. Rainfall in inches averaged: May 5.68, June 2.63, July 4.86, August 2.62, September 4.49. Effectiveness of the test chemicals on the European red mite and the twospotted spider mite was evaluated by counting the mites several times during the season on samples of 20 leaves/tree, 80 leaves/treatment. The effect of sprays on the predator S. punctum was evaluated by 3-min counts of adults and larvae around the periphery of the test trees. Effectiveness of chemicals on fruit feeders was assessed by scoring for injury all drops after July 1 and two picked samples, Aug 16 and 30. Apple samples averaged 121 fruits/replicate, 484/treatment002E
Nitrites and nitrates from food additives and natural sources and cancer risk: results from the NutriNet-Santé cohort
Authors: Chazelas Eloi , Pierre Fabrice , Druesne-Pecollo Nathalie , Esseddik Younes , Szabo de Edelenyi Fabien , Agaesse Cédric , De Sa Alexandre , Lutchia Rebecca , Gigandet Stéphane , Srour Bernard , Debras Charlotte , Huybrechts Inge , Julia Chantal , Kesse-Guyot Emmanuelle , Allès Benjamin , Galan Pilar , Hercberg Serge , Deschasaux-Tanguy Mélanie , Touvier Mathilde 
Published: March 2022

AbstractBackgroundNitrates and nitrites occur naturally in water and soil. They are also used as food additives (preservatives) in processed meats. They could play a role in the carcinogenicity of processed meat. The objective was to investigate the relationship between nitrate and nitrite intakes (natural food, water and food additive sources) and cancer risk in a large prospective cohort with detailed dietary assessment.MethodsOverall, 101    056 adults from the French NutriNet-Santé cohort (2009–ongoing, median follow-up 6.7 years) were included. Nitrites/nitrates exposure was evaluated using repeated 24-h dietary records, linked to a comprehensive composition database and accounting for commercial names/brands of industrial products. Associations with cancer risk were assessed using multi-adjusted Cox hazard models.ResultsIn total, 3311 incident cancer cases were diagnosed. Compared with non-consumers, high consumers of food additive nitrates had higher breast cancer risk [hazard ratio (HR) = 1.24 (95% CI 1.03–1.48), P = 0.02], more specifically for potassium nitrate. High consumers of food additive nitrites had higher prostate cancer risk [HR = 1.58 (1.14–2.18), P = 0.008], specifically for sodium nitrite. Although similar HRs were observed for colorectal cancer for additive nitrites [HR = 1.22 (0.85–1.75)] and nitrates [HR = 1.26 (0.90–1.76)], no association was detected, maybe due to limited statistical power for this cancer location. No association was observed for natural sources.ConclusionFood additive nitrates and nitrites were positively associated with breast and prostate cancer risks, respectively. Although these results need confirmation in other large-scale prospective studies, they provide new insights in a context of lively debate around the ban of these additives from the food industry.
Persistent Antibody Responses Up to 18 Months After Mild Severe Acute Respiratory Syndrome Coronavirus 2 Infection
Authors: Choe Pyoeng Gyun , Hong Jisu , Park Jiyoung , Chang Euijin , Kang Chang Kyung , Kim Nam Joong , Lee Chang Han , Park Wan Beom , Oh Myoung don 
Published: March 2022

Abstract

Background
Humoral immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may wane rapidly in persons recovered from mild coronavirus disease 2019 (COVID-19), but little is known about the longevity.

Methods
Serum samples were obtained 8, 12, and 18 months after infection from 20 patients with mild COVID-19. The binding activities of serum antibodies (immunoglobulin [Ig]A, IgG, and IgM) against SARS-CoV-2 antigens of the Wuhan-1 reference strain (wild-type) and the B.1.1.7, P.1, B.1.167.2, and B.1.1.529 variants were measured by enzyme-linked immunosorbent assays. Neutralizing antibody titers were measured using a cytopathic effect-based live virus neutralization assay.

Results
Serum IgA and IgG antibodies against spike or receptor-binding domain (RBD) protein of wild-type SARS-CoV-2 were detected for up to 18 months, and neutralizing antibodies persisted for 8 to 18 months after infection. However, any significant antibody responses against RBD proteins of SARS-CoV-2 variants were not observed, and median neutralizing antibody titers against the Delta variant at 8, 12, and 18 months were 8- to 11-fold lower than against wild-type viruses (P&lt;.001).

Conclusions
Humoral immunity persisted for up to 18 months after SARS-CoV-2 infection in patients with mild COVID-19. However, humoral immune activity against more recently circulating variants was reduced in this population.
From random to predictive: a context-specific interaction framework improves selection of drug protein–protein interactions for unknown drug pathways
Authors: Wilson Jennifer L , Gravina Alessio , Grimes Kevin 
Published: March 2022

Abstract
With high drug attrition, protein–protein interaction (PPI) network models are attractive as efficient methods for predicting drug outcomes by analyzing proteins downstream of drug targets. Unfortunately, these methods tend to overpredict associations and they have low precision and prediction performance; performance is often no better than random (AUROC ~0.5). Typically, PPI models identify ranked phenotypes associated with downstream proteins, yet methods differ in prioritization of downstream proteins. Most methods apply global approaches for assessing all phenotypes. We hypothesized that a per-phenotype analysis could improve prediction performance. We compared two global approaches—statistical and distance-based—and our novel per-phenotype approach, ‘context-specific interaction’ (CSI) analysis, on severe side effect prediction. We used a novel dataset of adverse events (or designated medical events, DMEs) and discovered that CSI had a 50% improvement over global approaches (AUROC 0.77 compared to 0.51), and a 76–95% improvement in average precision (0.499 compared to 0.284, 0.256). Our results provide a quantitative rationale for considering downstream proteins on a per-phenotype basis when using PPI network methods to predict drug phenotypes.
Definitive outcomes in patients with rifampicin-resistant tuberculosis treated in Niger from 2012 to 2019: A retrospective cohort study
Authors: Souleymane Mahamadou Bassirou , Decroo Tom , Mamadou Saïdou , Soumana Alphazazi , Lawan Ibrahim Mamane , Gagara-Issoufou Assiatou , Adehossi Eric , Ortuño-Gutiérrez Nimer , Lynen Lutgarde , Rigouts Leen , de Jong Bouke Catherine , Van Deun Armand , Piubello Alberto 
Published: March 2022

Abstract

Background
Outcomes of retreatment for rifampicin-resistant tuberculosis (RR-TB) are rarely reported. We report ‘definitive outcomes’ after a cascade approach to RR-TB treatment. After a bacteriologically adverse outcome for the 9-months fluoroquinolone-based Short Treatment Regimen (STR), patients were retreated with a bedaquiline-based regimen (BDQ-regimen).

Methods
A Retrospective cohort study of RR-TB patients treated with the STR during 2012–2019 and retreated with a BDQ-regimen in case of failure or relapse was conducted. Definitive relapse-free cure took into account BDQ-regimen outcomes.

Results
Of 367 patients treated with the STR, 20 (5.4%) experienced failure or relapse. Out of these 20 patients, 14 started a BDQ-regimen, of whom none experienced failure or relapse. Definitive end of treatment outcomes of STR after revising with third-line BDQ-regimen outcomes, 84.7% (311/367) were cured relapse-free, 10.6% (39/367) died during treatment and 3.0% (11/367) were lost to follow-up during treatment with either the STR or BDQ-regimen. Six patients (1.6%; 6/367) with STR failure/relapse died before starting a BDQ-regimen. No patient had definitive treatment failure or relapse and remained without treatment.

Conclusions
If fluoroquinolone resistance is excluded or rare, it is beneficial to use fluoroquinolone as the core drug for a first RR-TB treatment regimen and to safeguard bedaquiline for those in need of retreatment.
Ownership-neutral or ownership-blind? The case of Polish state-owned enterprises in EU merger control
Authors: Svetlicinii Alexandr 
Published: March 2022

Abstract
The article discusses the challenges associated with the assessment of economic concentrations involving state-owned enterprises (SOEs) under the European Union (EU) merger control. It reveals inconsistencies in ascertaining the exercise of and the (anti)competitive effects stemming from the state control over the SOEs caused by the strategic use of the ‘single economic unit’ concept in cases involving both European and non-European SOEs. Using the example of Poland and its economic statecraft, the article demonstrates how the use of various ownership-based and regulatory mechanisms employed by the State allows it to preserve control over strategic industries and enterprises. The study suggests that insufficient attention to the state ownership and state control in the EU merger control may create a risk of anti-competitive market distortions caused by the SOE-led industrial policies of the Member States to the detriment of the functioning of the internal market.
Developing an algorithm across integrated healthcare systems to identify a history of cancer using electronic medical records
Authors: Gander Jennifer C , Maiyani Mahesh , White Larissa L , Sterrett Andrew T , Güney Brianna , Pawloski Pamala A , DeFor Teri , Olsen YuanYuan , Rybicki Benjamin A , Neslund-Dudas Christine , Sheth Darsheen , Krajenta Richard , Purushothaman Devaki , Honda Stacey , Yonehara Cyndee , Goddard Katrina A B , Prado Yolanda K , Ahsan Habibul , Kibriya Muhammad G , Aschebrook-Kilfoy Briseis , Chan Chun-Hung , Hague Sarah , Clarke Christina L , Thompson Brooke , Sawyer Jennifer , Gaudet Mia M , Feigelson Heather Spencer 
Published: March 2022

AbstractObjectiveTumor registries in integrated healthcare systems (IHCS) have high precision for identifying incident cancer but often miss recently diagnosed cancers or those diagnosed outside of the IHCS. We developed an algorithm using the electronic medical record (EMR) to identify people with a history of cancer not captured in the tumor registry to identify adults, aged 40–65 years, with no history of cancer.Materials and MethodsThe algorithm was developed at Kaiser Permanente Colorado, and then applied to 7 other IHCS. We included tumor registry data, diagnosis and procedure codes, chemotherapy files, oncology encounters, and revenue data to develop the algorithm. Each IHCS adapted the algorithm to their EMR data and calculated sensitivity and specificity to evaluate the algorithm’s performance after iterative chart review.ResultsWe included data from over 1.26 million eligible people across 8 IHCS; 55 601 (4.4%) were in a tumor registry, and 44848 (3.5%) had a reported cancer not captured in a registry. The common attributes of the final algorithm at each site were diagnosis and procedure codes. The sensitivity of the algorithm at each IHCS was 90.65%–100%, and the specificity was 87.91%–100%.DiscussionRelying only on tumor registry data would miss nearly half of the identified cancers. Our algorithm was robust and required only minor modifications to adapt to other EMR systems.ConclusionThis algorithm can identify cancer cases regardless of when the diagnosis occurred and may be useful for a variety of research applications or quality improvement projects around cancer care.
Calcium-sensing receptor is not expressed in the absorptive enterocytes of weaned piglets
Authors: Zhao Xiaoya , Hui Qianru , Azevedo Paula , Nyachoti Charles Martin , O Karmin , Yang Chengbo 
Published: March 2022

Abstract
The calcium-sensing receptor (CaSR) is a kokumi receptor that plays an essential role in nutrient sensing and animal physiology, growth, and development. Pig CaSR (pCaSR) was identified and characterized in the intestine. However, further research is still needed to confirm the expression of CaSR in the epithelial cells isolated from weaned piglets. In this study, primary enterocytes were isolated and characterized from the ileum of weaned piglets by the Weiser distended intestinal sac technique and fluorescence-activated cell sorting (FACS) based on sucrase-isomaltase (SI) as an enterocyte-specific marker. The expression of CaSR was investigated in both primary enterocytes and the intestinal porcine enterocyte cell line-j2 (IPEC-J2) by droplet digital polymerase chain reaction (ddPCR), immunofluorescence staining, and Western blotting. Results demonstrated that porcine enterocytes could be obtained using FACS with the SI as the enterocyte-specific marker and that pCaSR is not expressed in both porcine ileal enterocytes and IPEC-J2 cells, which specifically identified the expression of pCaSR in ileal enterocytes with sensitive and specific approaches.
Designing an Intervention Trial of Human-Tick Encounters and Tick-Borne Diseases in Residential Settings Using 4-Poster Devices to Control Ixodes scapularis (Acari: Ixodidae): Challenges for Site Selection and Device Placement
Authors: Connally Neeta P , Rowe Adam , Kaufman Alison , Meek James I , Niesobecki Sara A , Hansen Amberjean P , White Jennifer , Nawrocki Courtney , Foster Erik , Hinckley Alison F , Eisen Lars 
Published: March 2022

Abstract
Blacklegged ticks, Ixodes scapularis Say, transmit Lyme disease spirochetes and other human pathogens in the eastern United States. White-tailed deer (Odocoileus virginianus) are key reproductive hosts for I. scapularis adults, and therefore control methods targeting deer have the potential for landscape-wide tick suppression. A topical acaricide product, containing 10% permethrin, is self-applied by deer to kill parasitizing ticks when they visit 4-Poster Tick Control Deer Feeders (hereafter, 4-Posters) Previous 4-Poster intervention studies, including in residential settings, demonstrated suppression of I. scapularis populations but did not include human-based outcomes. To prepare for a proposed 4-Poster intervention trial in residential areas of Connecticut and New York that would include human-tick encounters and tick-borne diseases as outcomes, we sought to identify areas (study clusters) in the 80–100 ha size range and specific locations within these areas where 4-Poster devices could be deployed at adequate density (1 device per 20–25 ha) and in accordance with regulatory requirements. Geographic Information System-based data were used to identify prospective study clusters, based on minimum thresholds for Lyme disease incidence, population density, and forest cover. Ground truthing of potential 4-Poster placement locations was done to confirm the suitability of selected clusters. Based on these efforts, we failed to identify more than a few residential areas fulfilling all criteria for a treatment cluster. We, therefore, reconsidered pursuing the intervention trial, which required inclusion of &gt;30 treatment clusters to achieve adequate statistical power. The 4-Poster methodology may be more readily evaluated in natural or public areas than in residential settings in NY or CT.
Mapping Exposure Diversity: The Divergent Effects of Algorithmic Curation on News Consumption
Authors: Jürgens Pascal , Stark Birgit 
Published: March 2022

Abstract
Diversity is a crucial precondition for a democratic public discourse. In today’s high-choice media environments, exposure to diverse news is largely determined by individuals’ personal selection. Yet these decisions are increasingly shaped by online platforms, whose curation mechanisms may serve to expand or contract the diversity of encountered content. In a major extension of existing research, we show that positive short-term effects of platforms mask detrimental long-term effects. Drawing on a four-month tracking dataset and a comprehensive content analysis covering the online news consumption of over 10,000 German citizens, we demonstrate that even though short-term usage of platforms uniformly increases exposure diversity, long-term reliance can lead to decreases. In addition, platforms vary in their influences: News aggregators are beneficial to exposure diversity, while Twitter and search engines have a limiting effect; Facebook offers no significant influence.
External jugular vein spontaneous aneurysm: a case report
Authors: El Youbi Samir , Naouli Hamza , Jiber Hamid , Bouarhroum Abdellatif 
Published: March 2022

AbstractVenous aneurysm of external jugular vein is very rare clinical entity. Often asymptomatic, the diagnosis may be suggested by clinical features and is usually confirmed by imaging. Surgical excision is indicated in symptomatic aneurysms and for esthetic reasons, other treatments such as endovascular treatment are being evaluated. We report a case of a 27-year-old woman with a saccular aneurysm of the right external jugular vein diagnosed by computerized tomogram angiography. The patient received successful surgical treatment.
PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins
Authors: Li Shuna , Li Qingqing , Tian Xiao , Mu Lijun , Ji Meiling , Wang Xiaoping , Li Na , Liu Fei , Shu Jing , Crawford Nigel M , Wang Yong 
Published: March 2022

AbstractWe have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.
Underlying mechanism of accelerated cell death and multiple disease resistance in a maizelethal leaf spot 1allele
Authors: Li Jiankun , Chen Mengyao , Fan Tianyuan , Mu Xiaohuan , Gao Jie , Wang Ying , Jing Teng , Shi Cuilan , Niu Hongbin , Zhen Sihan , Fu Junjie , Zheng Jun , Wang Guoying , Tang Jihua , Gou Mingyue 
Published: March 2022

AbstractMultiple disease resistance (MDR) in maize has attracted increasing attention. However, the interplay between cell death and metabolite changes and their contributions to MDR remains elusive in maize. In this study, we identified a mutant named as lesion mimic 30 (les30) that showed ‘suicidal’ lesion formation in the absence of disease and had enhanced resistance to the fungal pathogen Curvularia lunata. Using map-based cloning, we identified the causal gene encoding pheophorbide a oxidase (PAO), which is known to be involved in chlorophyll degradation and MDR, and is encoded by LETHAL LEAF SPOT1 (LLS1). LLS1 was found to be induced by both biotic and abiotic stresses. Transcriptomics analysis showed that genes involved in defense responses and secondary metabolite biosynthesis were mildly activated in leaves of the les30 mutant without lesions, whilst they were strongly activated in leaves with lesions. In addition, in les30 leaves with lesions, there was overaccumulation of defense-associated phytohormones including jasmonic acid and salicylic acid, and of phytoalexins including phenylpropanoids, lignin, and flavonoids, suggesting that their biosynthesis was activated in a lesion-dependent manner. Taken together, our study implies the existence of an interactive amplification loop of interrupted chlorophyll degradation, cell death, expression of defense-related genes, and metabolite changes that results in suicidal lesion formation and MDR, and this has the potential to be exploited by genetic manipulation to improve maize disease resistance.