bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi
Authors: Franco Cairo João Paulo L , Leonardo Flávia C , Alvarez Thabata M , Ribeiro Daniela A , Büchli Fernanda , Costa-Leonardo Ana M , Carazzolle Marcelo F , Costa Fernando F , Paes Leme Adriana F , Pereira Gonçalo AG , Squina Fabio M 
Published: November 2011

AbstractBackgroundLignocellulosic materials have been moved towards the forefront of the biofuel industry as a sustainable resource. However, saccharification and the production of bioproducts derived from plant cell wall biomass are complex and lengthy processes. The understanding of termite gut biology and feeding strategies may improve the current state of biomass conversion technology and bioproduct production.ResultsThe study herein shows comprehensive functional characterization of crude body extracts fromCoptotermes gestroialong with global proteomic analysis of the termite's digestome, targeting the identification of glycoside hydrolases and accessory proteins responsible for plant biomass conversion. The crude protein extract fromC. gestroiwas enzymatically efficient over a broad pH range on a series of natural polysaccharides, formed by glucose-, xylose-, mannan- and/or arabinose-containing polymers, linked by various types of glycosidic bonds, as well as ramification types. Our proteomic approach successfully identified a large number of relevant polypeptides in theC. gestroidigestome. A total of 55 different proteins were identified and classified into 29 CAZy families. Based on the total number of peptides identified, the majority of components found in theC. gestroidigestome were cellulose-degrading enzymes. Xylanolytic enzymes, mannan- hydrolytic enzymes, pectinases and starch-degrading and debranching enzymes were also identified. Our strategy enabled validation of liquid chromatography with tandem mass spectrometry recognized proteins, by enzymatic functional assays and by following the degradation products of specific 8-amino-1,3,6-pyrenetrisulfonic acid labeled oligosaccharides through capillary zone electrophoresis.ConclusionsHere we describe the first global study on the enzymatic repertoire involved in plant polysaccharide degradation by the lower termiteC. gestroi. The biochemical characterization of whole body termite extracts evidenced their ability to cleave all types of glycosidic bonds present in plant polysaccharides. The comprehensive proteomic analysis, revealed a complete collection of hydrolytic enzymes including cellulases (GH1, GH3, GH5, GH7, GH9 and CBM 6), hemicellulases (GH2, GH10, GH11, GH16, GH43 and CBM 27) and pectinases (GH28 and GH29).
It is time to consider third‐line options in antiretroviral‐experienced paediatric patients?
Authors: van Zyl Gert U , Rabie Helena , Nuttall James J , Cotton Mark F 
Published: November 2011

BackgroundThe historic use of full‐dose ritonavir as part of an unboosted protease inhibitor (PI)‐based antiretroviral therapy regimen in some South African children contributes to the frequent accumulation of major PI resistance mutations.MethodsIn order to describe the prevalence of major PI resistance in children failing antiretroviral therapy and to investigate the clinical, immunological and virological outcomes in children with PI resistance, we conducted a cross‐sectional study, with a nested case series, following up those children with major PI resistance. The setting was public health sector antiretroviral clinics in the Western Cape province of South Africa, and the subjects were children failing antiretroviral therapy. The following outcome measures were investigated: CD4 count, viral load and resistance mutations.ResultsFourteen (17%) of 82 patients, referred from tertiary hospitals, had major PI resistance. All these patients were exposed to regimens that included ritonavir as a single PI. Immune reconstitution and clinical benefit were achieved when using a lopinavir/ritonavir‐based treatment regimen in these children with prior PI resistance. At first HIV‐1 viral load follow up after initial resistance testing (n = 11), only one patient had a viral load of less than 400 copies/ml; at a subsequent follow up (n = 9), the viral loads of five patients were less than 400 copies/ml. Patients retained on LPV/r had lower viral loads than those switched to a non‐nucleoside reverse transcriptase inhibitor (NNRTI). However, two of three patients with follow‐up resistance tests accumulated additional PI resistance.ConclusionsIn children with pre‐existing PI resistance, although initially effective, the long‐term durability of a lopinavir/ritonavir‐based treatment regimen can be compromised by the accumulation of resistance mutations. Furthermore, a second‐line NNRTI regimen is often not durable in these patients. As genotypic resistance testing and third‐line treatment regimens are costly and limited in availability, we propose eligibility criteria to identify patients with high risk for resistance and guidance on drug selection for children who would benefit from third‐line therapy.
Characterization and potential functional significance of human-chimpanzee large INDEL variation
Authors: Polavarapu Nalini , Arora Gaurav , Mittal Vinay K , McDonald John F 
Published: November 2011

Abstract

Background
Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. It has been hypothesized that the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. To test the hypothesis that large INDELs (80 to 12,000 bp) may have contributed significantly to differences in gene regulation between the two species, we categorized human-chimpanzee INDEL variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression.

Results
Extensive, large INDEL variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.

Conclusions
The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.
Reduction in hospital-wide mortality after implementation of a rapid response team: a long-term cohort study
Authors: Beitler Jeremy R , Link Nate , Bails Douglas B , Hurdle Kelli , Chong David H 
Published: November 2011

Abstract
Introduction
Rapid response teams (RRTs) have been shown to reduce cardiopulmonary arrests outside the intensive care unit (ICU). Yet the utility of RRTs remains in question, as most large studies have failed to demonstrate a significant reduction in hospital-wide mortality after RRT implementation.

Methods
A cohort design with historical controls was used to determine the effect on hospital-wide mortality of an RRT in which clinical judgment, in addition to vital-signs criteria, was widely promoted as a key trigger for activation. All nonprisoner patients admitted to a tertiary referral public teaching hospital from 2003 through 2008 were included. In total, 77, 021 admissions before RRT implementation (2003 through 2005) and 79, 013 admissions after RRT implementation (2006 through 2008) were evaluated. The a priori primary outcome was unadjusted hospital-wide mortality. A Poisson regression model was then used to adjust for hospital-wide mortality trends over time. Secondary outcomes defined a priori were unadjusted out-of-ICU mortality and out-of-ICU cardiopulmonary-arrest codes.

Results
In total, 855 inpatient RRTs (10.8 per 1, 000 hospital-wide discharges) were activated during the 3-year postintervention period. Forty-seven percent of RRTs were activated for reasons of clinical judgment. Hospital-wide mortality decreased from 15.50 to 13.74 deaths per 1, 000 discharges after RRT implementation (relative risk, 0.887; 95% confidence interval (CI), 0.817 to 0.963; P = 0.004). After adjusting for inpatient mortality trends over time, the reduction in hospital-wide mortality remained statistically significant (relative risk, 0.825; 95% CI, 0.694 to 0.981; P = 0.029). Out-of-ICU mortality decreased from 7.08 to 4.61 deaths per 1, 000 discharges (relative risk, 0.651; 95% CI, 0.570 to 0.743; P < 0.001). Out-of-ICU cardiopulmonary-arrest codes decreased from 3.28 to 1.62 codes per 1, 000 discharges (relative risk, 0.493; 95% CI, 0.399 to 0.610; P < 0.001).

Conclusions
Implementation of an RRT in which clinical judgment, in addition to vital-signs criteria, was widely cited as a rationale for activation, was associated with a significant reduction in hospital-wide mortality, out-of-ICU mortality, and out-of-ICU cardiopulmonary-arrest codes. The frequent use of clinical judgment as a criterion for RRT activation was associated with high RRT utilization.
Randomized Controlled Trial of Kangaroo Care: Cardiorespiratory and Thermal Effects on Healthy Preterm Infants
Authors: Ludington-Hoe Susan , Anderson Gene Cranston , Swinth Joan , Thompson Carol , Hadeed Anthony 
Published: November 2011

Purpose:To determine the safety and effects on healthy preterm infants of three continuous hours of kangaroo care (KC) compared to standard NICU care by measuring cardiorespiratory and thermal responses.Design:Randomized controlled trial—pretest-test-posttest control group design.Sample:Twenty-four healthy preterm infants (33–35 weeks gestation at birth) nearing discharge. Eleven of the infants received KC; 13 received standard NICU care.Main Outcome Variables:Heart rate, respiratory rate, oxygen saturation, and abdominal skin temperature were manually recorded every minute. Apnea, bradycardia, periodic breathing, and regular breathing were captured continuously on a pneumocardiogram printout. Three consecutive interfeeding intervals (three hours each) on one day constituted the pretest, test, and posttest periods.Results:Mean cardiorespiratory and temperature outcomes remained within clinically acceptable ranges during KC. Apnea, bradycardia, and periodic breathing were absent during KC. Regular breathing increased for infants receiving KC compared to infants receiving standard NICU care.
The Premie-Neuro: A Clinical Neurologic Examination of Premature Infants
Authors: Daily Donna Kathryn , Ellison Patricia 
Published: November 2011

Purpose: To develop a neurologic assessment tool, the Premie-Neuro, for very low birth weight (VLBW) infants.Instrument Development: Neurologic data were collected during the course of the NICU stay. Factor analysis was utilized to determine the strength of relationships between items and to reduce the initial number of test items.Sample: An NICU cohort of 86 preterm infants was enrolled. Mean birth weight was 1,165.8 ± 446.7 grams, and mean gestational age at birth was 28.8 ± 3.2 weeks.Method: Seventy-five neurologic and behavioral characteristics were assessed in week 1 of life and every 2 weeks thereafter until 38 weeks postconceptional age.Main Outcome Variable: Three factors, the Neurologic Scale, the Movement Scale, and the Responsiveness Scale, described the neurologic examination.Results: Factor reliability was calculated for internal consistency (Cronbach alpha coefficient) and ranged from .73 to .82. The Premie-Neuro can be utilized with VLBW infants to monitor neurologic development during NICU care.
Newborn Screening Guidelines for the Critically Ill Infant
Authors: Balk Katherine 
Published: November 2011

The use of mass spectrometry in newborn screening has made possible the early diagnosis of various metabolic diseases. However, because aminoglycosides, blood transfusions, nothing by mouth status, and the presence of heparinized solutions all affect the results of newborn screens, neonates in critical care units who receive such treatments ought to be screened under specific practice guidelines. Many of the devastating sequelae of metabolic diseases are preventable if diagnosed early, making the development of such practice guidelines for use in the NICU especially important.Additionally, no standardized practice guidelines presently exist for determining who, whether birth hospital or primary care provider, is responsible for notifying the parent of a positive result and thus ensuring invaluable follow-up care. Such standardized guidelines for screening practice are needed to prevent devastating neurologic sequelae for children whose condition may otherwise escape unaddressed. Newborn screening guidelines developed at Johns Hopkins Hospital and Memorial Regional Hospital provide a helpful starting point.
Are Supine Chest and Abdominal Radiographs the Best Way to Confirm PICC Placement in Neonates?
Authors: Sneath Nicole 
Published: November 2011

Background: Peripherally inserted central catheters (PICCs) are commonly used in NICUs. Although they have many benefits, they also have many potential complications. Confirming catheter tip position is essential to decreasing complications, but the best method to achieve confirmation is unclear.Objectives: Literature review for studies that address line position confirmation to assist health care providers in evaluating the available research and to identify gaps in the literature.Method: A literature search of four major databases followed by an ancestry approach was performed. Articles reviewed specifically discuss PICC lines and PICC line placement confirmation.Results: Data on confirming PICC placement were lacking. Fluoroscopic placement is ideal, but cannot be done at the bedside and is costly. Supine chest radiograph is the most widely used method and is convenient, but when line tip position is unclear, contrast or ultrasound confirmation can be used. When PICC lines are placed in the saphenous vein, infants may benefit from supine and lateral abdominal radiographs to ensure placement in the inferior vena cava.Discussion: More studies are needed to generalize findings. PICC line tips should be located in the superior vena cava or inferior vena cava close to the junction with the right atrium (0.5–1 cm outside of the cardiac chambers in premature infants and 1–2 cm outside of the cardiac chambers in larger infants). Arm position is very important when performing radiographs for placement because movement of the arm can cause migration of the catheter. There is also significant inter-observer variability when identifying line tip position.
Complementary and Alternative Methods of Increasing Breast Milk Supply for Lactating Mothers of Infants in the NICU
Authors: Jackson Pamela 
Published: November 2011

“Breastfeeding” an infant in the NICU means that the mother must manually pump her breasts for milk for weeks to months until the infant is physiologically mature enough to suckle at the breast. Complementary and alternative therapies have been proposed to assist with lactation in NICU mothers. These methods for increasing breast milk supply include herbal galactagogues, kangaroo mothering, and relaxation therapies.A review of the literature was performed using PubMed and CINAHL databases. Twenty-four sources were chosen for inclusion in this article. Search terms included the following:galactagogues, breastfeeding, kangaroo care, andlactation, among others. The state of the science of alternative therapies in the management of inadequate breast milk supply is summarized here. The evidence is discussed and adverse side effects related to these therapies is addressed.
Mothers’ Breastfeeding Experiences in the NICU
Authors: Boucher Camille A. , Brazal Paola M. , Graham-Certosini Cynthia , Carnaghan-Sherrard Kathryn , Feeley Nancy 
Published: November 2011

AbstractPurpose: There is extensive literature on the physical and physiologic benefits of breastfeeding premature infants. Less is known about mothers’ perceptions of their own breastfeeding experience. This study explored the maternal experience of breastfeeding initiation and progression in the NICU.Design: A qualitative, descriptive design.Sample: A convenience sample of ten mothers was recruited from a Level III NICU. The sample included mothers of infants between 33 and 36 weeks gestational time at the time of the interview who had been in the NICU for at least five days.Main Outcome Variable: Mothers’ breastfeeding experiences with preterm infants in an NICU.Results: Mothers described their breastfeeding experiences in terms of maintaining milk production, the regimen of the NICU, mother as learner, personal motivation, and forming attachments.
Characterization of Unconventional Gas Play in the Lower Beluga
Authors: Gorney David , Jebutu Segun , Li Weidong , Cairo Rolando Del , Woods James , Manuel Ela 
Published: November 2011

Abstract
The response of NMR in the unconventional gas play in the Beluga formation of the Cook Inlet basin at Ninilchik Gas Field does not match the conventional predicted pressure and temperature model, because the zones are at a relatively shallow depth of 1500 to 3200 vertical feet and the pressure gradient is approximately 0.44 psi/ft. This paper presents insights and results of applications of NMR in these unconventional low-pressure hydrocarbon formations. The integration of NMR with other LWD logs, including density, neutron, and acoustic, showed the need for combined petrophysics and petrofacies interpretation.
NMR measurements exhibited that the free-fluid T2 cutoff was around 110 ms, well above the usual 33 ms for sandstone. Low pressure gas produces an NMR signal that not only is weaker but one that also relaxes faster than it does at high pressure. This is because of reduced hydrogen index and enhanced diffusion effects as pressure reduces.
The crossover of density and NMR porosity curves was used to identify the pay zones. The difference of the porosities is due to the gas hydrogen index effect, resulting in a crossover similar to density and neutron crossover. Unlike neutron, NMR porosity is mineralogy independent. Therefore, it may be more reliable than neutron-density crossover to identify gas. Porosity and gas saturation were computed based on the differences between apparent density porosity and apparent NMR porosity - the density and NMR crossover methodology (DMR).
Density and neutron logs were acquired while drilling and in the presence of dissolved gas trapped in formation porous space. Using the equations summarizing density and NMR porosity log sensitivities, the DMR method was applied to correct for the gas effect. The DMR method, with the help of additional logs such as neutron and density, enhances the understanding of NMR responses on these formation conditions. Once DMR porosity is computed, the free-fluid index can be recomputed to its actual value after gas correction; and gas-corrected permeability can now be estimated from the calibrated Coates-Timur model. Gas-corrected porosity and NMR permeability improved accuracy in determining the actual lithology.
Superior Quality Diamond Heel Inserts Improve Cutting Structure and Seal Life in Abrasive and Directional Applications
Authors: Cobb Tyler , Scott Dan , Nelms Derek 
Published: November 2011

Abstract
Polycrystalline diamond compact (PDC) bit technology and the application of PDC bits continues to improve and consequently, the window of application for roller-cone bits is being narrowed. This paper will demonstrate how in this narrowed window of tougher application focus, operators can gain additional performance and economic benefits by employing the latest design methods and materials including a new generation of diamond enhanced inserts.
The primary applications of focus where roller-cone bits are still predominantly used in achieving high buildup rates and for drilling through difficult formations such as highly abrasive sections, high interfacial severity (interbedded), and conglomerates. With increasing demands on roller-cone bit technology to handle damaging side and cyclical loading in directional applications, traditional roller-cone cutting structures exhibit premature rates of wear and damage on the outermost (heel row) tungsten carbide inserts (TCI). The loss of useable heel inserts allows for more direct formation contact, resulting in heat and wear in the seal area leading to premature seal failures. The development of improved designs and use of a new generation of superior quality diamond inserts has resulted in extended cutting structure life and consequently, longer seal life for operators.
A Practical Numerical Model to Optimize the Productivity of Multistage Fractured Horizontal Wells in the Cardium Tight Oil Resource
Authors: Sennhauser Eric S. , Wang Shunyi Jimmy , Liu Xiangping Mike 
Published: November 2011

Abstract
The technology to multi-stage fracture horizontal wells has opened up development of tight hydrocarbon resources world wide. One such resource in Canada is the Cardium Formation which extends over 3.5 million acres and has an estimated OOIP of over 10 billion barrels. The new technology has allowed accessing these tight resources which were previously uneconomic to develop with vertical wells. For the Cardium it is particularly true for the halo (or periphery) where reservoir quality was insufficient for economic depletion with vertical wells. This paper demonstrates an efficient model and methodology to optimize multi-stage fractured horizontal wells and provides production forecasts. A quarter of a fracture numerical simulation method (Quarter-Frac Model) with multi-phase and multi-dimensional characteristics is utilized in this paper to simulate the fluid flow from the repetitive drainage element in a full field development. The model uses an accurate description of the reservoir in terms of geology, fluid characteristics, and pressure profile. The overall performance of the multi-stage fractured horizontal well is determined by a range of completion variables that include well spacing, fracture spacing, fracture dimensions and characteristics, and placement of first and last fracture. The simulations are carried out for a range of completion and development variables. The results are then translated into the performance of the whole horizontal well. The optimum completion and development scenario depends on economic considerations.
It is realized that the first and last fractures (toe and heel) will have different drainage areas compared to those of the inside fractures. This is demonstrated by comparing the Quarter-Frac Model to an All-Frac Model simulating an actual horizontal well length with multiple fractures simulated with local grid refinement. A penetration ratio is introduced that describes the effect of placing fractures nearer to the section boundaries. The quarter-fracture model is shown to be efficient and provides reservoir engineers with a practical and accurate tool to design and optimize multi-stage fractured horizontal wells.
The quarter-fracture model has applications for primary and secondary recovery. Simulation results for the Cardium Formation have shown rapid pressure decline with primary depletion in full field development. An improvement in recovery can be achieved with pressure maintenance. Some preliminary simulation results are provided that show the effect of water injection which will be piloted in the field to demonstrate the feasibility.