bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Studies of Chloroplast Ribonucleases
Authors: Schuster Gadi , Stern David 
Published: March 2022

Gene regulation at the RNA level encompasses multiple mechanisms in prokaryotes and eukaryotes, including splicing, editing, endo- and exonucleolytic cleavage, and various phenomena related to small or interfering RNAs. Ribonucleases are key players in nearly all of these post-transcriptional mechanisms, as the catalytic agents. This proposal continued BARD-funded research into ribonuclease activities in the chloroplast, where RNase mutation or deficiency can cause metabolic defects and is often associated with plant chlorosis, embryo or seedling lethality, and/or failure to tolerate nutrient stress. The first objective of this proposal was to examined a series of point mutations in the PNPase enzyme of Arabidopsis both in vivo and in vitro. This goal is related to structure-function analysis of an enzyme whose importance in many cellular processes in prokaryotes and eukaryotes has only begun to be uncovered. PNPase substrates are mostly generated by endonucleolytic cleavages for which the catalytic enzymes remain poorly described. The second objective of the proposal was to examine two candidate enzymes, RNase E and RNase J. RNase E is well-described in bacteria but its function in plants was still unknown. We hypothesized it catalyzes endonucleolytic cleavages in both RNA maturation and decay. RNase J was recently discovered in bacteria but like RNase E, its function in plants had yet to be explored. The results of this work are described in the scientific manuscripts attached to this report. We have completed the first objective of characterizing in detail TILLING mutants of PNPase Arabidopsis plants and in parallel introducing the same amino acids changes in the protein and characterize the properties of the modified proteins in vitro. This study defined the roles for both RNase PH core domains in polyadenylation, RNA 3’-end maturation and intron degradation. The results are described in the collaborative scientific manuscript (Germain et al 2011). The second part of the project aimed at the characterization of the two endoribonucleases, RNase E and RNase J, also in this case, in vivo and in vitro. Our results described the limited role of RNase E as compared to the pronounced one of RNase J in the elimination of antisense transcripts in the chloroplast (Schein et al 2008; Sharwood et al 2011). In addition, we characterized polyadenylation in the chloroplast of the green alga Chlamydomonas reinhardtii, and in Arabidopsis (Zimmer et al 2009). Our long term collaboration enabling in vivo and in vitro analysis, capturing the expertise of the two collaborating laboratories, has resulted in a biologically significant correlation of biochemical and in planta results for conserved and indispensable ribonucleases. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture.
Functional genomics of reproduction and division of labor in a key non-Apis pollinator
Authors: Bloch Guy , Robinson Gene E. , Band Mark 
Published: March 2022

i. List the original objectives, as defined in the approved proposal, and any revisions made at the beginning or during the course of project. Our objectives were: 1) develop state-of-the-art functional genomics tools for B. terrestris. These resources will be then used to: 2) characterize genes and molecular pathways that are associated with reproduction, 3) characterize genes and molecular pathways associated with specialization in foraging or nursing activities, and 4) determine the extent to which juvenile hormone (JH) is involved in the regulation of reproduction and division of labor. 5) Use RNA interference to down regulate genes associated with reproductive physiology, division of labor, or both. A decrease in the cost of RNA sequencing enabled us to further use the BARD support to extend our research to three additional related projects: A) The regulation of body size which is crucial for understanding both reproduction (castedetermination) and (size based) division of labor in bumblebees. B) Analyze RNA editing in our RNA sequencing data which improves the molecular understanding of the systems we study. C) The influence of JH on the fat body in addition to the brain on which we focused in our proposal. The fat body is a key tissue regulating insect reproduction and health. ii. Background to the topic. Bees are by far the most important pollinators in agricultural and natural ecosystems. The recent collapse of honey bee populations, together with declines in wild bee (including bumble bee) populations, puts their vital pollination services under severe threat. A promising strategy for circumventing this risk is the domestication and mass-rearing of non-Apis bees. This approach has been successfully implemented for several bumble bees including Bombusterrestris in Israel, and B. impatiens in the US, which are mass-reared in captivity. In spite of their critical economic and environmental value, little is known about the physiology and molecular biology of bumble bees. In this collaborative project we developed functional genomics tools for the bumble bee B. terrestris and use these tools for a first thorough study on the physiology and molecular biology of reproduction, dominance, and division of labor in a bumble bee. iii. Major conclusions, solutions. The valuable molecular data of this project together with the functional tools and molecular information generated in this BARD funded project significantly advanced the understanding of bumblebee biology which is essential for maintaining their vital pollination services for US and Israel agriculture.
Characterization and Control Strategies of Low Pathogenic Avian Influenza Virus H9N2
Authors: Perk Simon , Mundt Egbert , Panshin Alexander , Davidson Irit , Shkoda Irina , AlTori Ameera , Garcia Maricarmen 
Published: March 2022

The avian influenza virus, subtype H9N2 subtype, defined as having a low pathogenicity, causes extensive economical losses in commercial flocks, probably due to management and synergism with other pathogens. AIV H9N2 was first identified in Israel in the year 2000, and since then it became endemic and widespread in Israel. Control by vaccination of commercial flocks with an inactivated vaccine has been introduced since 2007. In face of the continuous H9N2 outbreaks, and the application of the vaccination policy, we aimed in the present study to provide a method of differentiating naturally infected from vaccinated animals (DIVA). The aim of the assay would be detect only antibodies created by a de-novo infection, since the inactivated vaccine virus is not reproducing, and might provide a simple tool for mass detection of novel infections of commercial flocks. To fulfill the overall aim, the project was designed to include four operational objectives: 1. Evaluation of the genetic evolution of AIV in Israel; 2. Assessment of the diagnostic value of an NS1 ELISA; 3. NS1 ELISA as evaluation criteria for measuring the efficacy of vaccination against H9N2 AIV; 4. Development of an AIV H9 subtype specific ELISA systems. Major conclusion and implications drawn from the project were: 1. A continuous genetic change occurred in the collection of H9N2 isolates, and new introductions were identified. It was shown thatthe differences between the HA proteins of viruses used for vaccine productionand local fieldisolatesincreasedin parallelwith the durationand intensity ofvaccine use, therefore, developing a differential assay for the vaccine and the wild type viruses was the project main aim. 2. To assess the diagnostic value of an NS1 ELISA we first performed experimental infection trials using representative viruses of all introductions, and used the sera and recombinant NS1 antigens of the same viruses in homologous and heterologous NS1 ELISA combination. The NS1 ELISA was evidently reactive in all combinations, and did not discriminate significantly between different groups. 3. However, several major drawbacks of the NS1 ELISA were recognized: a) The evaluation of the vaccination effect in challenged birds, showed that the level of the NS1 antibodies dropped due to the vaccination-dependent virus level drop; b) the applicability of the NS1-ELISA was verified on sera of commercial flocks and found to be unusable due to physico-chemical composition of the sera and the recombinant antigen, c) commercial sera showed non-reactivity that might be caused by many factors, including vaccination, uncertainty regarding the infection time, and possibly low antigen avidity, d) NS1 elevated antibody levels for less than 2 months in SPF chicks. Due to the above mentioned reasons we do not recommend the application of the DIVA NS1 ELISA assay for monitoring and differentiation AIV H9N2 naturally-infected from vaccinated commercial birds.
Nutrition of the Developing Chick Embryo: Nutrient Uptake Systems of the Yolk Sac Membrane and Embryonic Intestine
Authors: Wong Eric A. , Uni Zehava 
Published: March 2022

We have examined the developmental changes in composition, amount, and uptake of yolk nutrients (fat, protein, water and carbohydrates) and the expression ofnutrient transporters in the yolk sac membrane (YSM) from embryonic day 11 (Ell) to 21 (E21) and small intestine from embryonic day 15 (E15) to E21 in embryos from young (22-25 wk) and old (45-50 wk) Cobb and Leghorn breeder flocks. The developmental expression profiles for the peptide transporter 1 (PepTl), the amino acid transporters, EAAT3, CAT-1 and BOAT, the sodium glucose transporter (SGLTl), the fructose transporter (GLUT5), the digestive enzymes aminopeptidase N (APN) and sucraseisomaltase (SI) were assayed by the absolute quantification real time PCR method in the YSM and embryonic intestine. Different temporal patterns of expression were observed for these genes. The effect of in ovo injection of peptides (the dipeptide Gly-Sar, purified peptides, trypsin hydrolysate) on transporter gene expression has been examined in the embryonic intestine. Injection of a partial protein hydrolysate resulted in an increase in expression of the peptide transporter PepT2. We have initiated a transcriptome analysis of genes expressed in the YSM at different developmental ages to better understand the function of the YSM.
Control of Bovine Anaplasmosis: Protective Capacity of the MSP2 Allelic Repertoire
Authors: Brayton Kelly A. , Shkap Varda , Palmer Guy H. , Brown Wendy C. , Molad Thea 
Published: March 2022

Anaplasmosis is an arthropod-borne disease of cattle caused by the rickettsia Anaplasmamarginale and is an impediment to efficient production of healthy livestock in both Israel and the United States. Currently, the only effective vaccines are derived from the blood of infected cattle. The risk of widespread transmission of both known and newly emergent pathogens has prevented licensure of live blood-based vaccines in the U.S. and is a major concern for their continued use in Israel. Consequently, development of a safe, effective vaccine is a high priority. Despite its drawbacks as a live, blood-based vaccine, the Israel vaccine strain protects against disease upon challenge with wild-type A. marginale in extensive experimental trials and during 50 years of deployment in Israel. Field studies in Australia and Argentina indicate that this protection is broadly effective. Thus, to identify antigens for development of a safe and effective recombinant vaccine, we have used a comparative genomics approach by sequencing the Israel vaccine strain and searching for shared surface antigens with sequenced wild-type U.S. strains. We have focused on Msp2, the immune-dominant but antigenically variable surface protein, based on shared structure among strains and demonstration that antibody from cattle immunized with the Israel vaccine strain binds Msp2 from the genetically and geographically distinct U.S. St. Maries strain, consistent with the ability to protect against St. Maries challenge. Importantly, we have defined the full repertoire of Msp2 simple variants encoded by the vaccine strain and hypothesize that a recombinant vaccine encoding this full repertoire will induce protection equivalent to that induced by the live vaccine strain. Any escape from immunity by generation of complex Msp2 variants is predicted to carry a severe fitness cost that prevents high-level bacteremia and disease— consistent with the type of protection induced by the live vaccine strain. We tested the hypothesis that the Msp2 simple variant repertoires in wild-type A. marginale strains are recognized by antibody from cattle immunized with the Israel vaccine strain and that immunization with the vaccine strain Msp2 repertoire can recapitulate the protection provided by the vaccine strain upon challenge with Israel and U.S. strains of A. marginale. Our findings demonstrate that a set of conserved outer membrane proteins are recognized by immune serum from A. centrale vaccinated animals but that this set of proteins does not include Msp2. These findings suggest that “subdominant” immunogens are required for vaccine induced protection.
KORELASI NILAI DAYA DUKUNG ULTIMIT TIANG BOR HASIL ANALISIS DENGAN HASIL PENGUJIAN PDA TEST (STUDI KASUS: PEMBANGUNAN JALAN TOL BOGOR RING ROAD SEKSI III A RUAS SIMPANG YASMIN - SIMPANG SALABENDA)
Authors: Rahman Ari Awalul , Hariati Feril , Chayati Nurul , Taqwa Fadhila Muhammad Libasut 
Published: March 2022

<p><strong>ABSTRAK</strong></p><p>Pondasi tiang <em>bored pile</em>, salah satu jenis pondasi yang biasanya digunakan untuk bangunan tinggi, atau bangunan dengan beban yang besar. Penentuan suatu pondasi ditentukan dengan mencari daya dukung beban maksimum atau daya dukung izin pada pondasi serta keamanan tiang, dengan kombinasi tahanan selimut dan tahanan ujung tiang diperlukan pengujian dinamis dan statik. Tujuan dari studi ini untuk membandingkan daya dukung tiang bor hasil analisis dengan nilai daya dukung PDA test. Menggunakan metode <em>Meyerhof, Decourt, </em>dan <em>Resee O’neill. </em>Berdasarkan data hasil PDA serta dilakukannya metode analisis menggunakan data N-SPT pada pembangunan di lokasi proyek jalan Tol Bogor Ring Road Seksi III A. Hasil <em>Root Means Square Error </em>daya dukung statis menggunakan metode <em>Meyerhof </em> R<sup>2</sup>= 0,1946, <em>Decourt </em>R<sup>2</sup>= 0,0077, dan <em>Resee O’neill </em>R<sup>2</sup>= 0,3795 dan hasil yang mendekati pada analisis daya dukung ultimit tiang statis menggunakan teori <em>Meyerhof </em>dan <em>Decourt</em>.</p><p align="center"><strong>ABSTRACT</strong></p><p>Bored pile foundation, a type of foundation that is usually used for tall buildings, or buildings with large loads. Determination of a foundation is determined by finding the maximum load bearing capacity or permit bearing capacity on the foundation and pile safety, with a combination of blanket resistance and pile end resistance required dynamic and static testing. This study aims to compare the bearing capacity of the drill pile as a result of the analysis with the PDA test carrying capacity using the Meyerhof, Decourt, and Resee O'neill methods. Based on PDA results data and analysis methods using N-SPT data on construction at the Bogor Ring Road Section III toll road project site A.Results of Root Means Square Error, static carrying capacity uses the Meyerhof R2 = 0.1946 method, Decourt R2 = 0.0077 , and Resee O'neill R2 = 0.3795 and the results are close to the ultimate bearing capacity analysis of static piles using Meyerhof and Decourtanalysis.</p><p> <strong><em>Keywords</em></strong><strong><em>: </em></strong><em>bored pile, pile bearing capacity, PDA test, N-SPT data, </em>metode <em>Meyerhof, Decourt, </em>and <em>Resee O’neill.</em><strong></strong></p>
Comparison of Two Pre-Hospital Stroke Scales to Detect Large Vessel Occlusion Strokes in Australia: A Prospective Observational Study
Authors: Ostman Cecilia , Garcia-Esperon Carlos , Lillicrap Thomas , Alanati Khaled , Chew Beng Lim Alvin , Pedler Jennifer , Edwards Sarah , Parsons Mark , Levi Christopher , Spratt Neil 
Published: March 2022

Aims The Hunter-8 and the ACT-FAST are stroke scales used in Australia for the pre-hospital identification of large vessel occlusion (LVO) stroke but have not previously been compared. Moreover, their use in identifying distal arterial occlusions has not previously been assessed. We therefore aimed to describe the area under the receiver operating curve (AUC) of the Hunter-8 versus the ACT-FAST for the detection of classic LVO. Methods Both scales were performed on consecutive patients presenting with stroke-like symptoms within 24 hours of symptom onset presenting to the emergency department at a tertiary referral hospital between June 2018 and January 2019. The AUC of the Hunter-8 and the ACT-FAST was calculated for the detection of LVO using different definitions [classic LVO (proximal segment of the middle cerebral artery (MCA-M1), terminal internal carotid artery (T-ICA), or tandem occlusions) and extended LVO (classic LVO plus proximal MCA-M2 and basilar occlusions)]. Results Of 126 suspected stroke patients, there were 24 classic LVO and 34 extended LVO. For detection of classic LVO, the Hunter-8 had an AUC of 0.79 and the ACT-FAST had an AUC of 0.77. For extended LVO, the AUC was 0.71 and 0.70 respectively. Conclusion Both scales represent a significant opportunity to identify patients with proven potential benefit from thrombectomy (classic LVO), however M2 and basilar occlusions may be more challenging to identify with these scales.
Crowdsourcing the Historical Record: Creating Linked Open Data for Chinese History at Scale
Authors: Sturgeon Donald 
Published: March 2022

An important part of the historical record of premodern China is recorded in historical works such as the standard dynastic histories. These works are a key source of knowledge about many aspects of premodern Chinese civilization, including persons, events, bureaucratic structures, literature, geography and astronomical observations. While many such sources have been digitized, typically these digitized texts encode only literal textual content and do not attempt to model the semantic content of the text. Similarly, while some of the historical data contained in some of these sources has been entered into specialist scholarly databases, an even greater proportion of the information does not yet exist in any machine-readable form. Producing such a machine-readable dataset of these materials requires the effort of many individuals working together due to the large scale of the task. This article introduces a crowdsourced approach in which annotation and knowledge base construction are carried out in parallel, with a knowledge base continually expanded through multi-user contributions to textual annotation immediately and automatically feeding back to provide improved assistance with subsequent annotation. The resulting knowledge base is dynamically exposed through Linked Open Data interfaces, creating a continually expanding machine-readable dataset covering around 3,000 years of recorded history.
Pengaruh Komposisi Sampah dan Feeding Rate terhadap Proses Biokonversi Sampah Organik oleh Larva Black Soldier Fly (BSF)
Authors: Hartono Rini , Anggrainy Anita Dwi , Bagastyo Arseto Yekti 
Published: March 2022

Biokonversi oleh larva Black Soldier Fly (BSF) menjadi metode pilihan untuk pengolahan sampah organik. Metode ini meliputi proses reduksi jumlah sampah yang dihasilkan masyarakat, pembentukan kompos dari residu sampah yang tidak terdegradasi oleh BSF, dan pertumbuhan larva BSF yang dapat digunakan untuk pakan hewan. Penelitian ini dilakukan untuk mengevaluasi seberapa besar pengaruh komposisi sampah dan feeding rate terhadap tingkat reduksi dan biokonversi sampah. Variabel penelitian berupa (i) komposisi sampah, yakni campuran 30% sampah sisa makanan (SM) dengan 70% sampah sayur (SY) atau sampah buah (B) atau sampah kebun (K), dan (ii) feeding rate (20, 35, dan 50 mg sampah organik/larva.hari). Penelitian ini dilakukan pada skala laboratorium selama 12 hari dengan menggunakan 300 ekor larva/bioreaktor. Hasil penelitian menunjukkan bahwa larva yang diberi campuran SM:SY dapat menghasilkan persentase reduksi sampah paling tinggi (81,98%), diikuti oleh campuran SM:B sebesar 81,23%, dan SM:K sebesar 42,71%. Ditinjau dari berat akhir larva, tingkat biokonversi tertinggi didapat pada campuran SM:B dan feeding rate 35 mg sampah/larva.hari, sedangkan tingkat biokonversi terendah didapat dari campuran SM:K dan feeding rate 50 mg sampah/larva.hari. Analisis protein menunjukkan bahwa semua larva BSF dari tiap campuran sampah layak dimanfaatkan sebagai pakan hewan, karena memiliki kandungan protein antara 34– 59%.

Bioconversion method using Black Soldier Fly (BSF) larvae has become of great interest in organic waste treatment. This method comprises of the municipal waste reduction process, the compost production from undegraded waste, and the growth of BSF larvae that can be used further as animal feed. This study evalutes the effect of waste composition and feeding rate on the waste reduction and bioconversion level. The evaluations were done on some variables: (i) waste composition (30% food waste and 70% vegetables waste (SY) or fruit waste (B) or garden waste (K), (ii) feeding rate (20, 35, and 50 mg waste/larva.day).The experiments were conducted in a laboratory scale for 12 days using 300 larvae/bioreactor. The results show that the larvae that has been fed with SM:SY obtained the highest waste reduction (81.98%), followed by SM:B (81.23%) and SM:K (42.71%). Based on the final larvae weight, the highest bioconversion level was acquired on the SM:B composition and feeding rate of 35 mg waste/larva.day, whereas the lowest bioconversion was measured on the SM:K composition and feeding rate of 50 mg waste/larva.day. The protein analyses describes that all larvae are applicable for animal feed due to protein contents of 34–59%.