bluuebunny/crossref_metadata_2025_split huggingface dataset:
PiHelper: an open source framework for drug-target and antibody-target data
Authors: Aksoy Bülent Arman , Gao Jianjiong , Dresdner Gideon , Wang Weiqing , Root Alex , Jing Xiaohong , Cerami Ethan , Sander Chris 
Published: June 2013

Abstract
Motivation: The interaction between drugs and their targets, often proteins, and between antibodies and their targets, is important for planning and analyzing investigational and therapeutic interventions in many biological systems. Although drug-target and antibody-target datasets are available in separate databases, they are not publicly available in an integrated bioinformatics resource. As medical therapeutics, especially in cancer, increasingly uses targeted drugs and measures their effects on biomolecular profiles, there is an unmet need for a user-friendly toolset that allows researchers to comprehensively and conveniently access and query information about drugs, antibodies and their targets.
Summary: The PiHelper framework integrates human drug-target and antibody-target associations from publicly available resources to help meet the needs of researchers in systems pharmacology, perturbation biology and proteomics. PiHelper has utilities to (i) import drug- and antibody-target information; (ii) search the associations either programmatically or through a web user interface (UI); (iii) visualize the data interactively in a network; and (iv) export relationships for use in publications or other analysis tools.
Availability: PiHelper is a free software under the GNU Lesser General Public License (LGPL) v3.0. Source code and documentation are at http://bit.ly/pihelper. We plan to coordinate contributions from the community by managing future releases.
Contact: pihelper@cbio.mskcc.org
Nondestructive and Continuous Monitoring of Oxygen Levels in Modified Atmosphere Packaged Ready‐to‐Eat Mixed Salad Products Using Optical Oxygen Sensors, and Its Effects on Sensory and Microbiological Counts during Storage
Authors: Hempel A. , O'Sullivan M. G. , Papkovsky D. B. , Kerry J. P. 
Published: June 2013

AbstractThe objective of this study was to determine the percentage oxygen consumption of fresh, respiring ready‐to‐eat (RTE) mixed leaf salad products (Iceberg salad leaf, Caesar salad leaf, and Italian salad leaf). These were held under different modified atmosphere packaging (MAP) conditions (5% O2, 5% CO2, 90% N2 (MAPC—commercial control), 21% O2, 5% CO2, 74% N2 (MAP 1), 45% O2, 5% CO2, 50% N2 (MAP 2), and 60% O2, 5% CO2, 35% N2 (MAP 3)) and 4 °C for up to 10 d. The quality and shelf‐life stability of all packaged salad products were evaluated using sensory, physiochemical, and microbial assessment. Oxygen levels in all MAP packs were measured on each day of analysis using optical oxygen sensors allowing for nondestructive assessment of packs. Analysis showed that with the exception of control packs, oxygen levels for all MAP treatments decreased by approximately 10% after 7 d of storage. Oxygen levels in control packs were depleted after 7 d of storage. This appears to have had no detrimental effect on either the sensory quality or shelf‐life stability of any of the salad products investigated. Additionally, the presence of higher levels of oxygen in modified atmosphere packs did not significantly improve product quality or shelf‐life stability; however, these additional levels of oxygen were freely available to fresh respiring produce if required. This study shows that the application of optical sensors in MAP packs was successful in nondestructively monitoring oxygen level, or changes in oxygen level, during refrigerated storage of RTE salad products.
Salt Reduction in Vegetable Fermentation: Reality or Desire?
Authors: Bautista‐Gallego J. , Rantsiou K. , Garrido‐Fernández A. , Cocolin L. , Arroyo‐López F. N. 
Published: June 2013

AbstractNaCl is a widely used chemical in food processing which affects sensory characteristics and safety; in fact, its presence is frequently essential for the proper preservation of the products. Because the intake of high contents of sodium is linked to adverse effects on human health, consumers demand foods with low‐sodium content. A 1st step to reduce the use of salt would imply the proper application of this compound, reducing its levels to those technologically necessary. In addition, different chloride salts have been evaluated as replacers for NaCl, but KCl, CaCl2, and ZnCl2 show the most promising perspectives of use. However, prior to any food reformulation, there is a need for exhaustive research before its application at industrial level. Salt reduction may lead to an increased risk in the survival/ growth of pathogens and may also alter food flavor and cause economic losses. This review deals with the technological, microbiological, sensorial, and health aspects of the potential low‐salt and salt‐substituted vegetable products and how this important segment of the food industry is responding to consumer demand.
RInSp: an r package for the analysis of individual specialization in resource use
Authors: Zaccarelli Nicola , Bolnick Daniel I. , Mancinelli Giorgio 
Published: June 2013

Summary

In the last decade, an increasing number of papers testifies a renewed interest in the topic of individual specialization in resource use and its implication at higher levels of ecological organization.

We present the package R Individual Specialization (RInSp) for the free open‐source statistical software r. RInSp provides a comprehensive set of classical and recently proposed indices for quantifying the degree of individual specialization using both categorical and continuous resource use data. The package also includes tools for ad hoc Monte Carlo and jackknife resampling procedures for significance testing, plotting and input/output data manipulation.

The use of RInSp is demonstrated by two examples. In addition, the potential of the package to be implemented beyond its original scope for multi‐level quantitative analyses of individual trait variance in natural communities is illustrated.
Acquisition of MDMA self‐administration: pharmacokinetic factors and MDMA‐induced serotonin release
Authors: Bradbury Sarah , Bird Judith , Colussi‐Mas Joyce , Mueller Melanie , Ricaurte George , Schenk Susan 
Published: June 2013

AbstractThe current study aimed to elucidate the role of pharmacokinetic (PK) parameters and neurotransmitter efflux in explaining variability in (±) 3, 4‐methylenedioxymethamphetamine (MDMA) self‐administration in rats. PK profiles of MDMA and its major metabolites were determined after the administration of 1.0 mg/kg MDMA (iv) prior to, and following, the acquisition of MDMA self‐administration. Synaptic levels of 5‐hydroxytryptamine (5HT) and dopamine (DA) in the nucleus accumbens were measured following administration of MDMA (1.0 and 3.0 mg/kg, iv) using in vivo microdialysis and compared for rats that acquired or failed to acquire MDMA self‐administration. Effects of the 5HT neurotoxin, 5,7 dihydroxytryptamine (5, 7‐DHT), on the acquisition of MDMA and cocaine self‐administration were also determined. In keeping with previous findings, approximately 50% of rats failed to meet a criterion for acquisition of MDMA self‐administration. The PK profiles of MDMA and its metabolites did not differ between rats that acquired or failed to acquire MDMA self‐administration. MDMA produced more overflow of 5HT than DA. The MDMA‐induced 5HT overflow was lower in rats that acquired MDMA self‐administration compared with those that did not acquire self‐administration. In contrast, MDMA‐induced DA overflow was comparable for the two groups. Prior 5,7‐DHT lesions reduced tissue levels of 5HT and markedly increased the percentage of rats that acquired MDMA self‐administration and also decreased the latency to acquisition of cocaine self‐administration. These data suggest that 5HT limits the initial sensitivity to the positively reinforcing effects of MDMA and delays the acquisition of reliable self‐administration.
Feeling Safe: A Metasynthesis of the Maternity Care Needs of Women Who Were Sexually Abused in Childhood
Authors: Montgomery Elsa 
Published: June 2013

AbstractBackgroundThe impact of childhood sexual abuse on birth experiences was highlighted 20 years ago in Birth. Subsequent accounts in the midwifery press testify to the emotional trauma that women who were sexually abused as children may suffer during childbirth and the potential for caregivers to make the situation worse. This study synthesizes research on the maternity care experiences of women who were sexually abused in childhood to answer the questions: what do women need during their childbearing experiences and what can health care practitioners do about it?MethodsA metasynthesis was conducted to integrate the findings of several qualitative studies. The eight eligible studies identified by database searches were closely read, recurring themes were extracted and compared across studies, and core themes were identified by means of an interpretative process of synthesis.ResultsThe key themes identified were control, remembering, vulnerability, dissociation, disclosure, and healing. If women were able to retain control and forge positive, trusting relationships with health care professionals, they felt safe and might experience healing in the process. “Safety” requires that women are not reminded of abusive situations. In the absence of control and trusting relationships, maternity care can be experienced as a re‐enactment of abuse.ConclusionsDuring their maternity care experience women who were sexually abused in childhood need to “feel safe.” Health care professionals can help them achieve this feeling by seeking to ensure that those experiences do not re‐enact abuse. (BIRTH 40:2 June 2013)
Adolescents' school‐related self‐concept mediates motor skills and psychosocial well‐being
Authors: Viholainen Helena , Aro Tuija , Purtsi Jarno , Tolvanen Asko , Cantell Marja 
Published: June 2013

BackgroundThe health benefits of exercise participation and physical activity for mental health and psychosocial well‐being (PSWB) have been shown in several studies. However, one important background factor, that is, motor skills (MSs), has largely been ignored. In addition, most of the existing research focuses on poor MSs, that is, poor MSs are often connected to poorer PSWB. The mechanism linking MSs and PSWB is unclear. However, a preliminary suggestion has been made that self‐worth or self‐perceptions might mediate the association between MSs and PSWB.AimWe investigated whether the self‐concepts (SCs) of school‐related physical education (SCPE), reading (SCR), and mathematics (SCM) mediate the relationship between MSs and PSWB in adolescence.MethodsThe study sample consisted of a second‐grade female cohort (N = 327), ranging in age between 12 and 16 (years) in a municipality in Central Finland. PSWB was measured by the Strengths and Difficulties Questionnaire and the school‐related SCs by the SC of ability scale adapted for use in Finland. MSs was assessed by a self‐reported adolescent version of the Developmental Coordination Disorder Questionnaire. Structural mediator modelling was used to test the associations between MSs and PSWB with SC as a mediator.ResultsFirst, MSs was strongly associated with school‐related SCPE and SCM. However, a mediator role was observed only for SCPE, which weakly mediated peer problems. Second, MSs and PSWB, especially conduct problems, showed a very strong direct association.ConclusionsThe study suggests that MSs is connected to PSWB in adolescent girls. Enhancement of MSs could be a preventive strategy for supporting PSWB in adolescent girls.
Short‐term patient reported health‐related quality of life (HRQL) outcomes after robot‐assisted radical cystectomy (RARC)
Authors: Poch Michael A. , Stegemann Andrew P. , Rehman Shabnam , Sharif Mohamed A. , Hussain Abid , Consiglio Joseph D. , Wilding Gregory E. , Guru Khurshid A. 
Published: June 2013

Objective
To determine short‐term health‐related quality of life (HRQL) outcomes after robot‐assisted radical cystectomy (RARC) using the Bladder Cancer Index (BCI) and European Organisation for Research and Treatment of Cancer (EORTC) Body Image Scale (BIS).
Patients and Methods
All patients undergoing RARC were enrolled in a quality assurance database.
The patients completed two validated questionnaires, BCI and BIS, preoperatively and at standardised postoperative intervals.
The primary outcome measure was difference in interval and baseline BCI and BIS scores.
Complications were identified and classified by Clavien grade.
Results
In all, 43 patients completed pre‐ and postoperative questionnaires
There was a decline in the urinary domain at 0–1 month after RARC (P = 0.006), but this returned to baseline by 1–2 months.
There was a decline in the bowel domain at 0–1 month (P < 0.001) and 1–2 months (P = 0.024) after RARC, but this returned to baseline by 2–4 months.
The decline in BCI scores was greatest for the sexual function domain, but this returned to baseline by 16–24 months after RARC.
Body image perception using BIS showed no significant change after RARC except at the 4–10 months period (P = 0.018).
Conclusions
Based on BCI and BIS scores HRQL outcomes after RARC show recovery of urinary and bowel domains ≤6 months. Longer follow‐up with a larger cohort of patients will help refine HRQL outcomes.
Supported housing for people with Down's syndrome
Authors: Cumella Stuart , Heslam Sheila 
Published: June 2013

Accessible summary

This is about people with Down's syndrome who live in supported housing.

Their parents said that they liked the help given by support staff to people with a learning disability.

They thought more help was needed with managing money and finding a job.

People had to wait a long time before they could get a place in supported housing.

Parents carried on giving help to their sons and daughters even after they had gone into supported housing.

Parents helped most with things like managing money and dealing with problems.

This means that people who live in supported housing who do not have parents find life more difficult.

SummaryThere has been limited research on the attitudes of family carers and the part they play in helping people with a learning disability choose accommodation. A postal questionnaire was sent to family carers of people with Down's Syndrome, to identify their attitudes to supported living, their experience of the application process, and the support they provided to residents. It was found that main family carers of people with Down's Syndrome in supported living were generally satisfied with the housing and support provided, particularly with respect to activities of daily living. There was less satisfaction with the help received with managing finance and employment. There had been a mean of 2 years delay between application and securing accommodation. The large number of people providing care at home who wished their family‐member to move into supported living suggests that there is a large unmet need for this type of accommodation. Almost all family carers continued to provide support after participants moved into supported living, particularly with more complex tasks such as financial management, and with responding to crises and ill‐health. This indicates that people with a learning disability in supported living who do not have active contact with their family may be vulnerable financially and less likely than others to receive help at times of crisis. The proportion of residents in supported living who experience such problems will increase as family carers die or otherwise become too infirm to continue to provide support.
Randomized phase II study of gemcitabine plus S‐1 versus S‐1 in advanced biliary tract cancer: A Japan Clinical Oncology Group trial (JCOG 0805)
Authors: Morizane Chigusa , Okusaka Takuji , Mizusawa Junki , Takashima Atsuo , Ueno Makoto , Ikeda Masafumi , Hamamoto Yasuo , Ishii Hiroshi , Boku Narikazu , Furuse Junji 
Published: June 2013

The oral fluoropyrimidine, S‐1, combined with or without gemcitabine is considered to be a promising agent for treating advanced biliary tract cancer; gemcitabine plus cisplatin is the current standard regimen. This randomized phase II trial was designed to evaluate the safety and efficacy of two regimens: gemcitabine plus S‐1 (GS) (gemcitabine: 1000 mg/m2, day 1 and day 8; S‐1: 60 mg/m2, twice daily on days 1–14, repeated every 3 weeks); and S‐1 (80 mg/m2, days 1–28, given orally twice daily for 4 weeks, followed by a 2‐week rest, repeated every 6 weeks). The regimen with a higher 1‐year survival would be selected for a subsequent phase III trial. Between February 2009 and April 2010, 101 patients were randomized. For the GS (n = 51) and S‐1 (n = 50) arms, the 1‐year survival was 52.9% (95% confidence interval, 38.5–65.5) and 40.0% (95% confidence interval, 26.5–53.1), and the median survival times were 12.5 and 9.0 months, respectively. Grade 3/4 hematological toxicities were more frequent in the GS arm (leucocytes 29.4%, neutrophils 60.8%, hemoglobin 11.8%, platelets 11.8%) than in the S‐1 arm (leucocytes 2.0%, neutrophils 4.0%, hemoglobin 4.0%, platelets 4.0%). Although two treatment‐related deaths occurred in the GS arm, all other grade 3/4 non‐hematological toxicities were reversible. In conclusion, GS was considered to be more promising and was selected as the test regimen for a subsequent phase III trial comparing GS with gemcitabine plus cisplatin combination therapy. This study was registered at the UMIN Clinical Trials Registry as UMIN 000001685 (http://www.umin.ac.jp/ctr/index.htm).
Permeability of Roads to Movement of Scrubland Lizards and Small Mammals
Authors: BREHME CHERYL S. , TRACEY JEFF A. , MCCLENAGHAN LEROY R. , FISHER ROBERT N. 
Published: June 2013

AbstractA primary objective of road ecology is to understand and predict how roads affect connectivity of wildlife populations. Road avoidance behavior can fragment populations, whereas lack of road avoidance can result in high mortality due to wildlife‐vehicle collisions. Many small animal species focus their activities to particular microhabitats within their larger habitat. We sought to assess how different types of roads affect the movement of small vertebrates and to explore whether responses to roads may be predictable on the basis of animal life history or microhabitat preferences preferences. We tracked the movements of fluorescently marked animals at 24 sites distributed among 3 road types: low‐use dirt, low‐use secondary paved, and rural 2‐lane highway. Most data we collected were on the San Diego pocket mouse (Chaetodipus fallax), cactus mouse (Peromyscus eremicus), western fence lizard (Sceloporus occidentalis), orange‐throated whiptail (Aspidoscelis hyperythra), Dulzura kangaroo rat (Dipodomys simulans) (dirt, secondary paved), and deer mouse (Peromyscus maniculatus) (highway only). San Diego pocket mice and cactus mice moved onto dirt roads but not onto a low‐use paved road of similar width or onto the highway, indicating they avoid paved road substrate. Both lizard species moved onto the dirt and secondary paved roads but avoided the rural 2‐lane rural highway, indicating they may avoid noise, vibration, or visual disturbance from a steady flow of traffic. Kangaroo rats did not avoid the dirt or secondary paved roads. Overall, dirt and secondary roads were more permeable to species that prefer to forage or bask in open areas of their habitat, rather than under the cover of rocks or shrubs. However, all study species avoided the rural 2‐lane highway. Our results suggest that microhabitat use preferences and road substrate help predict species responses to low‐use roads, but roads with heavy traffic may deter movement of a much wider range of small animal species.
Costs and Benefits of the Presence of Leopards to the Sport‐Hunting Industry and Local Communities in Niassa National Reserve, Mozambique
Authors: JORGE AGOSTINHO A. , VANAK ABI T. , THAKER MARIA , BEGG COLLEEN , SLOTOW ROB 
Published: June 2013

AbstractSport hunting is often proposed as a tool to support the conservation of large carnivores. However, it is challenging to provide tangible economic benefits from this activity as an incentive for local people to conserve carnivores. We assessed economic gains from sport hunting and poaching of leopards (Panthera pardus), costs of leopard depredation of livestock, and attitudes of people toward leopards in Niassa National Reserve, Mozambique. We sent questionnaires to hunting concessionaires (n = 8) to investigate the economic value of and the relative importance of leopards relative to other key trophy‐hunted species. We asked villagers (n = 158) the number of and prices for leopards poached in the reserve and the number of goats depredated by leopard. Leopards were the mainstay of the hunting industry; a single animal was worth approximately U.S.$24,000. Most safari revenues are retained at national and international levels, but poached leopard are illegally traded locally for small amounts ($83). Leopards depredated 11 goats over 2 years in 2 of 4 surveyed villages resulting in losses of $440 to 6 households. People in these households had negative attitudes toward leopards. Although leopard sport hunting generates larger gross revenues than poaching, illegal hunting provides higher economic benefits for households involved in the activity. Sport‐hunting revenues did not compensate for the economic losses of livestock at the household level. On the basis of our results, we propose that poaching be reduced by increasing the costs of apprehension and that the economic benefits from leopard sport hunting be used to improve community livelihoods and provide incentives not to poach.Costos y Beneficios de la Presencia de Leopardos para la Industria de la Caza Deportiva y las Comunidades Locales en Niassa, Reserva Nacional, Mozambique
Assessing the Potential to Restore Historic Grazing Ecosystems with Tortoise Ecological Replacements
Authors: GRIFFITHS CHRISTINE J. , ZUËL NICOLAS , JONES CARL G. , AHAMUD ZAIRABEE , HARRIS STEPHEN 
Published: June 2013

AbstractThe extinction of large herbivores, often keystone species, can dramatically modify plant communities and impose key biotic thresholds that may prevent an ecosystem returning to its previous state and threaten native biodiversity. A potentially innovative, yet controversial, landscape‐based long‐term restoration approach is to replace missing plant‐herbivore interactions with non‐native herbivores. Aldabran giant (Aldabrachelys gigantea) and Madagascan radiated (Astrochelys radiata) tortoises, taxonomically and functionally similar to the extinct Mauritian giant tortoises (Cylindraspis spp.), were introduced to Round Island, Mauritius, in 2007 to control the non‐native plants that were threatening persistence of native species. We monitored the response of the plant community to tortoise grazing for 11 months in enclosures before the tortoises were released and, compared the cost of using tortoises as weeders with the cost of using manual labor. At the end of this period, plant biomass; vegetation height and cover; and adult, seedling, flower, and seed abundance were 3–136 times greater in adjacent control plots than in the tortoise enclosures. After their release, the free‐roaming tortoises grazed on most non‐native plants and significantly reduced vegetation cover, height, and seed production, reflecting findings from the enclosure study. The tortoises generally did not eat native species, although they consumed those native species that increased in abundance following the eradication of mammalian herbivores. Our results suggest that introduced non‐native tortoises are a more cost‐effective approach to control non‐native vegetation than manual weeding. Numerous long‐term outcomes (e.g., change in species composition and soil seed bank) are possible following tortoise releases. Monitoring and adaptive management are needed to ensure that the replacement herbivores promote the recovery of native plants.Estudiando el Potencial para Restaurar Ecosistemas Históricos de Forrajeo con Reemplazos Ecológicos de Tortugas Terrestres