bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry
Authors: Brauchle Michael , Hansen Simon , Caussinus Emmanuel , Lenard Anna , Ochoa-Espinosa Amanda , Scholz Oliver , Sprecher Simon G. , Plückthun Andreas , Affolter Markus 
Published: November 2014

ABSTRACT
Protein–protein interactions are crucial for cellular homeostasis and play important roles in the dynamic execution of biological processes. While antibodies represent a well-established tool to study protein interactions of extracellular domains and secreted proteins, as well as in fixed and permeabilized cells, they usually cannot be functionally expressed in the cytoplasm of living cells. Non-immunoglobulin protein-binding scaffolds have been identified that also function intracellularly and are now being engineered for synthetic biology applications. Here we used the Designed Ankyrin Repeat Protein (DARPin) scaffold to generate binders to fluorescent proteins and used them to modify biological systems directly at the protein level. DARPins binding to GFP or mCherry were selected by ribosome display. For GFP, binders with KD as low as 160 pM were obtained, while for mCherry the best affinity was 6 nM. We then verified in cell culture their specific binding in a complex cellular environment and found an affinity cut-off in the mid-nanomolar region, above which binding is no longer detectable in the cell. Next, their binding properties were employed to change the localization of the respective fluorescent proteins within cells. Finally, we performed experiments in Drosophila melanogaster and Danio rerio and utilized these DARPins to either degrade or delocalize fluorescently tagged fusion proteins in developing organisms, and to phenocopy loss-of-function mutations. Specific protein binders can thus be selected in vitro and used to reprogram developmental systems in vivo directly at the protein level, thereby bypassing some limitations of approaches that function at the DNA or the RNA level.
Phospho-regulated Drosophila adducin is a determinant of synaptic plasticity in a complex with Dlg and PIP2 at the larval neuromuscular junction
Authors: Wang Simon Ji Hau , Tsai Amy , Wang Mannan , Yoo SooHyun , Kim Hae-yoon , Yoo Byoungjoo , Chui Vincent , Kisiel Marta , Stewart Bryan , Parkhouse Wade , Harden Nicholas , Krieger Charles 
Published: November 2014

ABSTRACT
Adducin is a ubiquitously expressed actin- and spectrin-binding protein involved in cytoskeleton organization, and is regulated through phosphorylation of the myristoylated alanine-rich C-terminal kinase (MARCKS)-homology domain by protein kinase C (PKC). We have previously shown that the Drosophila adducin, Hu-li tai shao (Hts), plays a role in larval neuromuscular junction (NMJ) growth. Here, we find that the predominant isoforms of Hts at the NMJ contain the MARCKS-homology domain, which is important for interactions with Discs large (Dlg) and phosphatidylinositol 4,5-bisphosphate (PIP2). Through the use of Proximity Ligation Assay (PLA), we show that the adducin-like Hts isoforms are in complexes with Dlg and PIP2 at the NMJ. We provide evidence that Hts promotes the phosphorylation and delocalization of Dlg at the NMJ through regulation of the transcript distribution of the PAR-1 and CaMKII kinases in the muscle. We also show that Hts interactions with Dlg and PIP2 are impeded through phosphorylation of the MARCKS-homology domain. These results are further evidence that Hts is a signaling-responsive regulator of synaptic plasticity in Drosophila.
Interaction of NANOS2 and NANOS3 with different components of the CNOT complex may contribute to the functional differences in mouse male germ cells
Authors: Suzuki Atsushi , Niimi Yuki , Saga Yumiko 
Published: November 2014

ABSTRACTNANOS2 and NANOS3 belong to the Nanos family of proteins that contain a conserved zinc finger domain, which consists of two consecutive CCHC-type zinc finger motifs, and contribute to germ cell development in mice. Previous studies indicate that there are redundant and distinct functions of these two proteins. NANOS2 rescues NANOS3 functions in the maintenance of primordial germ cells, whereas NANOS3 fails to replace NANOS2 functions in the male germ cell pathway. However, the lack of a conditional allele of Nanos3 has hampered delineation of each contribution of NANOS2 and NANOS3 to the male germ cell pathway. In addition, the molecular mechanism underlying the distinct functions of these proteins remains unexplored. Here, we report an unexpected observation of a transgenic mouse line expressing a NANOS2 variant harboring mutations in the zinc finger domain. Transcription of Nanos2 and Nanos3 was strongly compromised in the presence of this transgene, which resulted in the mimicking of the Nanos2/Nanos3 double-null condition in the male gonad. In these transgenic mice, P-bodies involved in RNA metabolism had disappeared and germ cell differentiation was more severely affected than that in Nanos2-null mice, indicating that NANOS3 partially substitutes for NANOS2 functions. In addition, similar to NANOS2, we found that NANOS3 associated with the CCR4-NOT deadenylation complex but via a direct interaction with CNOT8, unlike CNOT1 in the case of NANOS2. This alternate interaction might account for the molecular basis of the functional redundancy and differences in NANOS2 and NANOS3 functions.
Temporally distinct roles of ATM and ROS in genotoxic-stress-dependent induction and maintenance of cellular senescence
Authors: Nair Raji R. , Bagheri Meisam , Saini Deepak Kumar 
Published: November 2014

ABSTRACT
Cells exposed to genotoxic stress induce cellular senescence through a DNA damage response (DDR) pathway regulated by ATM kinase and reactive oxygen species (ROS). Here, we show that the regulatory roles for ATM kinase and ROS differ during induction and maintenance of cellular senescence. Cells treated with different genotoxic agents were analyzed using specific pathway markers and inhibitors to determine that ATM kinase activation is directly proportional to the dose of the genotoxic stress and that senescence initiation is not dependent on ROS or the p53 status of cells. Cells in which ROS was quenched still activated ATM and initiated the DDR when insulted, and progressed normally to senescence. By contrast, maintenance of a viable senescent state required the presence of ROS as well as activated ATM. Inhibition or removal of either of the components caused cell death in senescent cells, through a deregulated ATM–ROS axis. Overall, our work demonstrates existence of an intricate temporal hierarchy between genotoxic stress, DDR and ROS in cellular senescence. Our model reports the existence of different stages of cellular senescence with distinct regulatory networks.
Integrated Care Management
Authors: Wilson Jo , Tingle John 
Published: November 2014

Some clinicians are at the leading edge of good practice in the introduction of integrated care management (ICM) (Wilson, 1996) based on partnership, quality and driven by performance. The new Government White Paper (Department of Health, 1997) outlines proposals for integrated care with all care planners and providers working collaboratively. A number of health and social care organizations have worked collaboratively to develop care programmes based on patient-centred care. One of the vehicles is multidisciplinary pathways of care (MPCs) which is the risk management tool for monitoring jointly agreed quality and patient outcome criteria from the performance of planning and providing individual patient care. ICM views the multidisciplinary approaches to collaborating care delivery by activity, cost and quality, and using a process approach to problemand outcome-based care delivery. Involving patients and their carers in determining the process and outcomes of care provides a route to better communication, patient and staff satisfaction and the overall quality of care. This article deals with the use of ICM through the monitoring system of multidisciplinary pathways of care (MPCs) as a tool for minimizing risk and improving the continuous quality improvement of patient care. MPCs are one of the components of ICM which need to incorporate clinical guidelines, protocols, interdisciplinary standards, evidenced-based practice and clinical outcomes which are continuously monitored across all sectors of care.
Compression Testing of Ultra-High-Performance Concrete
Authors: Graybeal Benjamin A. 
Published: November 2014

Abstract
The compressive mechanical response of ultra-high-performance concrete (UHPC) surpasses that exhibited by the types of concrete for which the ASTM C39 compressive strength test and ASTM C469 compression modulus of elasticity test were developed. When attempting to complete these tests on UHPC, one will likely face challenges related to both the required load rate of 35 psi/s (0.25 MPa/s) and the cylinder end preparation requirements. Compression strength test durations for concretes with compressive strengths up to and exceeding 29 ksi (200 MPa) can be excessively long. Common cylinder end preparation techniques are not acceptable because of the high strength of the concrete, resulting in the requirement that the cylinder ends be ground to a plane, parallel finish. Researchers at the U.S. Federal Highway Administration are developing solutions to these challenges. Research on the compressive strength of UHPC has demonstrated that the strength determined through the use of an ASTM C109 type of test on concrete cubes is very similar to the strength reported with ASTM C39 tests on cylinders. Thus cubes, which do not require end preparation, can be used as a surrogate for cylinders. A separate study investigating the effect of increasing the load rate during cylinder compressive tests to 150 psi/s (1 MPa/s) was also completed. In this testing program, 400 cylinders with strengths between 18 and 30 ksi (124 and 200 MPa) were tested at a range of load rates. The strength and modulus of elasticity increases resulting from the load rate increase were observed to be minimal.
Tensile Mechanical Response of Ultra-High-Performance Concrete
Authors: Graybeal Benjamin A. 
Published: November 2014

Abstract
The tensile mechanical response of ultra-high-performance concrete (UHPC) is distinctly different from conventional concretes and traditional fiber-reinforced concretes. UHPC can exhibit a pseudo-strain-hardening behavior wherein the fiber reinforcement bridging tensile cracks is sufficient to allow for a sustained tensile capacity at stress levels near the tensile-matrix-cracking strength through significant tensile-strain levels. This mechanical response is generating interest in the structural design community; however, quantification of the response through standardized test methods is necessary. Researchers at the U.S. Federal Highway Administration have developed a test that directly measures the tensile response of UHPC-class materials. This test, conceptually similar to the ASTM E8 [ASTM E8-13a: Standard Test Methods for Tension Testing of Metallic Materials, Annual Book of ASTM Standards, ASTM International, West Conshohocken, PA, 2013] test for steel, provides a method to assess the tensile response from elastic behaviors through multi-cracking and eventual crack localization. Prismatic specimens are loaded in direct tension under a fixed-end condition, allowing cast or extracted specimens to be tested under conditions that mimic the tensile loading that can occur within full-scale structural elements. Testing to date has assessed two UHPC matrices and a variety of fiber types/dosages with promising results in terms of test-procedure robustness.
Compressibility and Durability Characteristics of Lime Treated Expansive Semiarid Soils
Authors: Moghal Arif Ali Baig , Kareem Obaid Ali Abdul , Al-Refeai Talal O. , Al-Shamrani Mosleh Ali 
Published: November 2014

Abstract
The current study evaluates the role of lime and the curing period on the compressibility and durability characteristics of two expansive semiarid soils samples originating from Saudi Arabia. The compressibility behavior of these soil samples was evaluated using a range of loading periods of time. Starting with a minimum practicable loading period of 0.5 h, the loading periods were progressively increased to 1, 2, 4, 8, and 24 h. It has been observed that the addition of lime significantly reduces the compressibility behavior of both the selected soils. The study shows that, for a given consolidation pressure increment, an increase in the duration of loading time produces a moderate increase in the final equilibrium void ratio values. In order to evaluate the durability characteristics, lime leachability tests (amount of lime that is converted into soluble form by dissociation into calcium and hydroxyl ions) were conducted on compacted specimens at varying lime contents on samples cured for 1, 7, 14, and 28 days. Analysis of the soil samples subject to increasing periods of curing time show a considerable decrease in the concentration of calcium. This is due to the transformation of amorphous lime into a stable crystalline form, which leads to the formation of pozzolanic compounds.
Evaluation of the Use of Recycled Concrete Aggregate in French Drain Systems
Authors: Nam Boo Hyun , Behring Zachary R. , Kim Jinyoung , Chopra Manoj , Shoucair John , Park Chul-Soo 
Published: November 2014

Abstract
Recycled concrete aggregate (RCA) is often used as a replacement for virgin aggregate in road foundations (base course), embankments, hot-mix asphalt, and Portland cement concrete. However, the use of RCA in exfiltration drainage systems, such as French drains, is still uncommon. The primary concerns with using RCA as drainage media are excessive fines and calcite precipitation that can cause a reduction in permeability performance. This study investigates the potential benefits of RCA as drainage material. This paper presents and discusses: (1) the results of a nationwide survey on current practices and policies, (2) physical and chemical properties, (3) effective fine-removing methods, (4) re-cementation potential, (4) permeability (under varied fine content), and (5) long-term drainage performance of RCA as drainage material. Test results indicate that RCA No. 4 gradation does not restrict the flow of water, but the RCA fines being generated during aggregate handling process (e.g., stockpiling, placing and transporting) may cause clogging buildup over time.
Adipose tissue, estradiol levels, and bone health in obese men with metabolic syndrome
Authors: Ornstrup Marie Juul , Kjær Thomas Nordstrøm , Harsløf Torben , Stødkilde-Jørgensen Hans , Hougaard David Michael , Cohen Arieh , Pedersen Steen Bønløkke , Langdahl Bente Lomholt 
Published: November 2014

ObjectiveVisceral adipose tissue (VAT) is associated with an increased risk of metabolic syndrome (MetS). Recent studies have suggested that VAT negatively affects bone. However, MetS has also been associated with higher estradiol (E2) levels, which is bone protective. We therefore investigated the impact of VAT and E2levels on bone density, structural parameters, and strength estimates.DesignA cross-sectional study was conducted in 72 obese men with MetS to investigate the impact of VAT and E2levels on bone.MethodsBone parameters were assessed by dual-energy X-ray absorptiometry (DXA), quantitative computed tomography (QCT), and high-resolution peripheral QCT (HRpQCT) at lumbar spine, proximal femur, radius, and tibia. VAT volume was measured by magnetic resonance imaging (MRI) and sexual hormones were measured in blood samples.ResultsMen with high VAT had a lower bone density at the hip (P<0.05), lower cortical thickness, and higher buckling ratio at femoral neck (FN) (P=0.008 andP=0.02), compared with men with low VAT, despite a similar body weight and BMI. Generally, E2levels were low (median 43 pmol/l), and men with E2levels below median had reduced bone density at lumbar spine (P=0.04), and impaired structural parameters at radius and tibia, compared with men with E2levels above median. At the hip, VAT volume and E2levels affected bone density independently and additively, and 50% of men with high VAT and low E2levels had osteopenia with significantly lowerT-score at FN (P=0.004).ConclusionsHigh VAT and low E2negatively affect bone in obese men with MetS. VAT and E2affect bone density at the hip independently and additively, revealing an unexpected high prevalence of osteopenia in middle-aged men with MetS.
Functional Variants in DPYSL2 Sequence Increase Risk of Schizophrenia and Suggest a Link to mTOR Signaling
Authors: Liu Yaping , Pham Xuan , Zhang Lilei , Chen Pei-lung , Burzynski Grzegorz , McGaughey David M , He Shan , McGrath John A , Wolyniec Paula , Fallin Margaret D , Pierce Megan S , McCallion Andrew S , Pulver Ann E , Avramopoulos Dimitrios , Valle David 
Published: November 2014

Abstract
Numerous linkage and association studies by our group and others have implicated DPYSL2 at 8p21.2 in schizophrenia. Here we explore DPYSL2 for functional variation that underlies these associations. We sequenced all 14 exons of DPYSL2 as well as 27 conserved noncoding regions at the locus in 137 cases and 151 controls. We identified 120 variants, eight of which we genotyped in an additional 729 cases and 1542 controls. Several were significantly associated with schizophrenia, including a three single-nucleotide polymorphism (SNP) haplotype in the proximal promoter, two SNPs in intron 1, and a polymorphic dinucleotide repeat in the 5′-untranslated region that alters sequences predicted to be involved in translational regulation by mammalian target of rapamycin signaling. The 3-SNP promoter haplotype and the sequence surrounding one of the intron 1 SNPs direct tissue-specific expression in the nervous systems of Zebrafish in a pattern consistent with the two endogenous dpysl2 paralogs. In addition, two SNP haplotypes over the coding exons and 3′ end of DPYSL2 showed association with opposing sex-specific risks. These data suggest that these polymorphic, schizophrenia-associated sequences function as regulatory elements for DPYSL2 expression. In transient transfection assays, the high risk allele of the polymorphic dinucleotide repeat diminished reporter expression by 3- to 4-fold. Both the high- and low-risk alleles respond to allosteric mTOR inhibition by rapamycin until, at high drug levels, allelic differences are eliminated. Our results suggest that reduced transcription and mTOR-regulated translation of certain DPYSL2 isoforms increase the risk for schizophrenia.
Evaluación de Insecticidas para el Manejo de Monalonion velezangeli, Carvalho & Costa (Hemiptera: Miridae) en Aguacate
Authors: Montilla Pérez Jimena , Londoño Zuluaga Martha Eugenia , Monsalve García Danilo Augusto , Correa Londoño Guillermo Antonio 
Published: November 2014

La chinche monalonion, coclicllo o chupanga (Monalonion velezangeli) causa daños en brotes terminales de aguacate, afectando el desarrollo del árbol; en frutos causa secamiento y, por lo tanto, rechazo en la comercialización. Aún no existen estrategias para el manejo de la plaga y los productores utilizan insecticidas sin previa evaluación de su efectividad. Se evaluaron insecticidas con un nuevo modo de acción sobre M. velezangeli bajo condiciones controladas. Se utilizó un diseño de bloques completos al azar, con once tratamientos y cuatro repeticiones. Los tratamientos fueron los insecticidas deltametrina, λ-cihalotrina, imidacloprid, thiametoxam, spinosad, spiromesifen, diflubenzurón, diafentiurón, una mezcla de thiametoxam + λ-cihalotrina; y además, un testigo relativo (agua) y un testigo absoluto (sin aplicación). La unidad experimental consistió de un arbusto de guayaba común con diez insectos confinados en una jaula de tela tul. Los tratamientos se aplicaron una vez con los insectos confinados en la jaula. Se identificó que deltametrina, λ-cihalotrina, thiametoxam, imidacloprid y la mezcla de thiametoxam más λ-cihalotrina causan mortalidad entre 85 y 100% sobre M. velezangeli, 24 horas después de ser aplicados y 3 días después la mortalidad alcanza el 100%. Estos productos pueden ser incluidos en un programa de manejo integrado para M. velezangeli. El diafentiurón causa mortalidades entre 51-81%. No se evidenció efecto de diafentiurón, diflubenzurón y spiromesifen sobre la progenie de adultos expuestos, pero ninfas tratadas que alcanzaron el estado adulto, dieron origen a un menor número de ninfas; sin embargo, este efecto debe dilucidarse mejor.
Characterization of Cocoa (Theobroma cacao L.) Farming Systems in the Norte de Santander Department and Assessment Their Sustainability
Authors: Ramírez Sulvarán Jesús Arturo , Sigarroa Rieche Alina Katil , Del Valle Vargas Rómulo Alberto 
Published: November 2014

The cocoa (Theobroma cacao L.) based economy has been considered a valid alternative to support sustainable development in northeastern Colombia. However, there is a lack of information about the cocoa production systems in the region which is needed for the implementation of effective plans to improve their performance and sustainability. Four of the main cocoa producing municipalities in the Norte de Santander department were considered for this study: Teorama, Bucarasica, Cúcuta and San Calixto. These entities were selected due to their adequate security conditions, availability of field assistants and departmental representativeness in cocoa production. The objective was to obtain basic information for local, specific and participatory actions for the sustainability of the cocoa production systems and to improve the living conditions of farmers. The methodology used was based on the farming system approach, considering the socioeconomic, technological and agro-ecological components, and their relationships, and evaluating them according to the principles of sustainable agriculture. The phases covered were: (1) analysis of secondary data, (2) formulation and evaluation of sustainability indicators, (3) design, implementation and analysis of survey data and (4) validation by the farmers of the obtained information and the prioritization of problems. The results indicate that there is only one cocoa production system of a family-mercantile type, with low technology. Most farmers have low incomes and basic needs such as health, education and public services are not met. They do not employ the agronomic and post-harvest practices recommended by specialists. The water and soil resources are being degraded. In general, the farming system leans towards unsustainability and it is vital that integrative actions be taken to change this situation.
Pre and Postharvest Enzymatic Activity in Gulupa (Passiflora edulis Sims) Fruits from the Colombian Lower Montane Rain Forest
Authors: Franco Germán , Cartagena Valenzuela José Régulo , Correa Londoño Guillermo Antonio , Rojano Benjamín Alberto , Piedrahita Correa Ana María , Ibarz Albert , Falguera Víctor 
Published: November 2014

“High-Andean fruits” are deemed important because of their potential for domestic consumption and exportation. Among them, gulupa (Passiflora edulis Sims) is an exotic fruit of good acceptance in European markets. However, the technological support associated with the crop is incipient and its short shelf life leads to rapid deterioration of the product. This fact makes it necessary to investigate the physical, physiological and biochemical processes that characterize fruit ripening, in order to take actions to ensure that it arrives in its best possible condition to the consumer. In this context, the current study aimed at identifying enzymatic activity in gulupa fruits during pre and postharvest. Plant material from the Colombian Gene Bank (administered by Corpoica) was used. Fruits of known age were periodically harvested to determine the activity of the enzymes α-amylase, polygalacturonase (PG), pectinmethylesterase (PME) and polyphenol oxidase (PPO) through destructive samplings. It was found that α-amylase and PG are linked to the increase of soluble solids, which favors the sweet taste of the fruit. In turn, the low activity of PPO enables agroindustrial processing without severe fruit browning.