bluuebunny/crossref_metadata_2025_split huggingface dataset:
Some Pragmatic Tips for Dealing With Clinical Uncertainty
Authors: Bernstein Ratner Nan 
Published: January 2011

PurposeThis article proposes some recommendations to enable clinicians to balance certainty and uncertainty when evaluating the currency and effectiveness of their treatment approaches.MethodI offer the following advice: (a) Question the authority of the information previously learned in one’s career; (b) be cognizant of what we do not yet know about best clinical practice; (c) understand that knowledge of “best practices” is both temporary and relative; (d) enable access to new information by the use of electronic alerts; (e) be flexible in reading new clinical reports, keeping an open mind as to their value; (f) get the clinically relevant details of new approaches by reading the full reports; and (g) employ, and then evaluate the outcomes of, new approaches used in treating individuals on our caseload.ResultsExamples are provided to show that proactive participation in research-alert programs can enable clinicians to access emerging, clinically relevant information, some of which is controversial. Staying abreast of such information is more efficient than performing guided searches for information as challenging cases arise.ConclusionsApplications of these recommendations should enable practicing clinicians to entertain new, clinically useful concepts while not taxing the limited time that clinicians typically have to engage in continuing education.
Balancing Certainty and Uncertainty in Clinical Practice
Authors: Kamhi Alan G. 
Published: January 2011

Purpose
In this article, I question how practitioners can balance the certainty and confidence that they can help their patients with the uncertainty that makes them continually question their beliefs and assumptions.

Method
I compare the mechanisms of science and models of clinical practice that may help practitioners achieve the right balance between total acceptance of the status quo and an open willingness to explore and accept new ideas.

Conclusion
Clinical practice, unlike science, has no independent self-correction mechanism that leads to consensus about best clinical practices. Evidence-based models provide principles and guidelines for clinical practice, but ultimately, clinical decisions may be influenced most by a practitioner’s epistemology (belief systems) and propensity for rational thinking.
Critical Thinking: Knowledge and Skills for Evidence-Based Practice
Authors: Finn Patrick 
Published: January 2011

Purpose
I respond to Kamhi’s (2011) conclusion in his article “Balancing Certainty and Uncertainty in Clinical Practice” that rational or critical thinking is an essential complement to evidence-based practice (EBP).

Method
I expand on Kamhi’s conclusion and briefly describe what clinicians might need to know to think critically within an EBP profession. Specifically, I suggest how critical thinking is relevant to EBP, broadly summarize the relevant skills, indicate the importance of thinking dispositions, and outline the various ways our thinking can go wrong.

Conclusion
I finish the commentary by suggesting that critical thinking skills should be considered a required outcome of our professional training programs.
Providing Written Language Services in the Schools: The Time Is Now
Authors: Fallon Karen A. , Katz Lauren A. 
Published: January 2011

Purpose
The current study was conducted to investigate the provision of written language services by school-based speech-language pathologists (SLPs). Specifically, the study examined SLPs' knowledge, attitudes, and collaborative practices in the area of written language services as well as the variables that impact provision of these services.

Method
Public school–based SLPs from across the country were solicited for participation in an online, Web-based survey. Data from 645 full-time SLPs from 49 states were evaluated using descriptive statistics and logistic regression.

Results

Many school-based SLPs reported not providing
any
services in the area of written language to students with written language weaknesses. Knowledge, attitudes, and collaborative practices were mixed. A logistic regression revealed three variables likely to predict high levels of service provision in the area of written language.

Conclusion
Data from the current study revealed that many struggling readers and writers on school-based SLPs' caseloads are not receiving services from their SLPs. Implications for SLPs' preservice preparation, continuing education, and doctoral preparation are discussed.
A Comparison of Oral and Written English Styles in African American Students at Different Stages of Writing Development
Authors: Ivy Lennette J. , Masterson Julie J. 
Published: January 2011

PurposeThe purpose of this investigation was to compare the rates of using African American English (AAE) grammatical features in spoken and written language at different points in literacy development. Based on Kroll’s model (1981), a high degree of similarity in use between the modalities was expected at Grade 3, and lower similarity was expected at Grade 8.MethodSpoken and written language samples were analyzed for the occurrence of 6 AAE morphosyntactic features. Fifteen third graders and 15 eighth graders were asked to respond to interview questions and to retell stories in both modalities. Percentage use of the AAE grammatical features and a dialectal density measure were used to measure rates of AAE occurrence.ResultsFindings indicated comparable use of dialect in spoken and written modalities for 3rdgraders, but a difference in use between the modalities for 8thgraders. The 8thgraders used more dialectal features in speaking than writing.ConclusionThese results suggest that there is likely a period in writing development when speakers of AAE learn to dialect switch in their writing.
Knowledge of Mathematical Equivalence in Children With Specific Language Impairment: Insights From Gesture and Speech
Authors: Mainela-Arnold Elina , Alibali Martha W. , Ryan Kristin , Evans Julia L. 
Published: January 2011

Purpose
This study investigated understanding of mathematical equivalence in children with and without specific language impairment (SLI).

Method
A total of 34 children (ages 8;1 [years;months] to 11;7), including 9 with expressive SLI (E-SLI), 8 with expressive and receptive SLI (ER-SLI), and 17 age-matched typically developing (TD) children completed addition and mathematical equivalence problems. The problem-solving strategies revealed in solutions and in gestural and verbal explanations were coded.

Results

The children with SLI were less accurate than their TD peers in solving addition and equivalence problems. None of the children in the ER-SLI group solved the equivalence problems correctly; however, the number of children who solved any of the equivalence problems correctly did not differ in the E-SLI and CA groups. Children in the ER-SLI group tended to express incorrect strategies for solving the equivalence problems in both gesture and speech, whereas children in the E-SLI group often expressed
correct
strategies in gestures, but
incorrect
strategies in speech.

Conclusion
Children with SLI showed delays in their knowledge of mathematical equivalence. Children with ER-SLI displayed greater delays than children with E-SLI. Children with E-SLI sometimes expressed more advanced knowledge in gestures, suggesting that their knowledge is represented in a nonverbal format.
Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains
Authors: Tian Yuan , Simanshu Dhirendra K. , Ma Jin-Biao , Patel Dinshaw J. 
Published: December 2010

Argonaute and Piwi proteins are key players in the RNA silencing pathway, with the former interacting with micro-RNAs (miRNAs) and siRNAs, whereas the latter targets piwi-interacting RNAs (piRNAs) that are 2′-O-methylated (2
′
-OCH
3
) at their 3′ ends. Germline-specific piRNAs and Piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. Humans contain four Piwi family proteins designated Hiwi1, Hiwi2, Hiwi3, and Hili. We report on the structures of Hili-PAZ (Piwi/Argonaute/Zwille) domain in the free state and Hiwi1 PAZ domain bound to self-complementary 14-mer RNAs (12-bp + 2-nt overhang) containing 2
′
-OCH
3
and 2′-OH at their 3′ ends. These structures explain the molecular basis underlying accommodation of the 2
′
-OCH
3
group within a preformed Hiwi1 PAZ domain binding pocket, whose hydrophobic characteristics account for the preferential binding of 2
′
-OCH
3
over 2′-OH 3′ ends. These results contrast with the more restricted binding pocket for the human Ago1 PAZ domain, which exhibits a reverse order, with preferential binding of 2′-OH over 2
′
-OCH
3
3′ ends.
Principal network analysis: identification of subnetworks representing major dynamics using gene expression data
Authors: Kim Yongsoo , Kim Taek-Kyun , Kim Yungu , Yoo Jiho , You Sungyong , Lee Inyoul , Carlson George , Hood Leroy , Choi Seungjin , Hwang Daehee 
Published: December 2010

Abstract
Motivation: Systems biology attempts to describe complex systems behaviors in terms of dynamic operations of biological networks. However, there is lack of tools that can effectively decode complex network dynamics over multiple conditions.
Results: We present principal network analysis (PNA) that can automatically capture major dynamic activation patterns over multiple conditions and then generate protein and metabolic subnetworks for the captured patterns. We first demonstrated the utility of this method by applying it to a synthetic dataset. The results showed that PNA correctly captured the subnetworks representing dynamics in the data. We further applied PNA to two time-course gene expression profiles collected from (i) MCF7 cells after treatments of HRG at multiple doses and (ii) brain samples of four strains of mice infected with two prion strains. The resulting subnetworks and their interactions revealed network dynamics associated with HRG dose-dependent regulation of cell proliferation and differentiation and early PrPSc accumulation during prion infection.
Availability: The web-based software is available at: http://sbm.postech.ac.kr/pna.
Contact: dhhwang@postech.ac.kr; seungjin@postech.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Discovering approximate-associated sequence patterns for protein–DNA interactions
Authors: Chan Tak-Ming , Wong Ka-Chun , Lee Kin-Hong , Wong Man-Hon , Lau Chi-Kong , Tsui Stephen Kwok-Wing , Leung Kwong-Sak 
Published: December 2010

Abstract
Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein–DNA interactions in transcriptional regulation. Extensive efforts have been made to better understand the protein–DNA interactions. Recent mining on exact TF–TFBS-associated sequence patterns (rules) has shown great potentials and achieved very promising results. However, exact rules cannot handle variations in real data, resulting in limited informative rules. In this article, we generalize the exact rules to approximate ones for both TFs and TFBSs, which are essential for biological variations.
Results: A progressive approach is proposed to address the approximation to alleviate the computational requirements. Firstly, similar TFBSs are grouped from the available TF–TFBS data (TRANSFAC database). Secondly, approximate and highly conserved binding cores are discovered from TF sequences corresponding to each TFBS group. A customized algorithm is developed for the specific objective. We discover the approximate TF–TFBS rules by associating the grouped TFBS consensuses and TF cores. The rules discovered are evaluated by matching (verifying with) the actual protein–DNA binding pairs from Protein Data Bank (PDB) 3D structures. The approximate results exhibit many more verified rules and up to 300% better verification ratios than the exact ones. The customized algorithm achieves over 73% better verification ratios than traditional methods. Approximate rules (64–79%) are shown statistically significant. Detailed variation analysis and conservation verification on NCBI records demonstrate that the approximate rules reveal both the flexible and specific protein–DNA interactions accurately. The approximate TF–TFBS rules discovered show great generalized capability of exploring more informative binding rules.
Availability: Supplementary Data are available on Bioinformatics online and http://www.cse.cuhk.edu.hk/.
Contact: tmchan@cse.cuhk.edu.hk
Cancer therapy design based on pathway logic
Authors: Layek Ritwik , Datta Aniruddha , Bittner Michael , Dougherty Edward R. 
Published: December 2010

AbstractMotivation: Cancer encompasses various diseases associated with loss of cell cycle control, leading to uncontrolled cell proliferation and/or reduced apoptosis. Cancer is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur in different ways and at different locations in a pathway. Consequently, therapy design should first identify the location and type of malfunction to arrive at a suitable drug combination.Results: We consider the growth factor (GF) signaling pathways, widely studied in the context of cancer. Interactions between different pathway components are modeled using Boolean logic gates. All possible single malfunctions in the resulting circuit are enumerated and responses of the different malfunctioning circuits to a ‘test’ input are used to group the malfunctions into classes. Effects of different drugs, targeting different parts of the Boolean circuit, are taken into account in deciding drug efficacy, thereby mapping each malfunction to an appropriate set of drugs.Contact: edward@ece.tamu.edu
Analysis of TETRAKETIDE α-PYRONE REDUCTASE Function in Arabidopsis thaliana Reveals a Previously Unknown, but Conserved, Biochemical Pathway in Sporopollenin Monomer Biosynthesis
Authors: Grienenberger Etienne , Kim Sung Soo , Lallemand Benjamin , Geoffroy Pierrette , Heintz Dimitri , Souza Clarice de Azevedo , Heitz Thierry , Douglas Carl J. , Legrand Michel 
Published: December 2010

Abstract
The precise structure of the sporopollenin polymer that is the major constituent of exine, the outer pollen wall, remains poorly understood. Recently, characterization of Arabidopsis thaliana genes and corresponding enzymes involved in exine formation has demonstrated the role of fatty acid derivatives as precursors of sporopollenin building units. Fatty acyl-CoA esters synthesized by ACYL-COA SYNTHETASE5 (ACOS5) are condensed with malonyl-CoA by POLYKETIDE SYNTHASE A (PKSA) and PKSB to yield α-pyrone polyketides required for exine formation. Here, we show that two closely related genes encoding oxidoreductases are specifically and transiently expressed in tapetal cells during microspore development in Arabidopsis anthers. Mutants compromised in expression of the reductases displayed a range of pollen exine layer defects, depending on the mutant allele. Phylogenetic studies indicated that the two reductases belong to a large reductase/dehydrogenase gene family and cluster in two distinct clades with putative orthologs from several angiosperm lineages and the moss Physcomitrella patens. Recombinant proteins produced in bacteria reduced the carbonyl function of tetraketide α-pyrone compounds synthesized by PKSA/B, and the proteins were therefore named TETRAKETIDE α-PYRONE REDUCTASE1 (TKPR1) and TKPR2 (previously called DRL1 and CCRL6, respectively). TKPR activities, together with those of ACOS5 and PKSA/B, identify a conserved biosynthetic pathway leading to hydroxylated α-pyrone compounds that were previously unknown to be sporopollenin precursors.
EXPO, an Exocyst-Positive Organelle Distinct from Multivesicular Endosomes and Autophagosomes, Mediates Cytosol to Cell Wall Exocytosis inArabidopsisand Tobacco Cells
Authors: Wang Juan , Ding Yu , Wang Junqi , Hillmer Stefan , Miao Yansong , Lo Sze Wan , Wang Xiangfeng , Robinson David G. , Jiang Liwen 
Published: December 2010

AbstractThe exocyst protein complex mediates vesicle fusion with the plasma membrane. By expressing an (X)FP-tagged Arabidopsis thaliana homolog of the exocyst protein Exo70 in suspension-cultured Arabidopsis and tobacco (Nicotiana tabacum) BY-2 cells, and using antibodies specific for Exo70, we detected a compartment, which we term EXPO (for exocyst positive organelles). Standard markers for the Golgi apparatus, the trans-Golgi network/early endosome, and the multivesicular body/late endosome in plants do not colocalize with EXPO. Inhibitors of the secretory and endocytic pathways also do not affect EXPO. Exo70E2-(X)FP also locates to the plasma membrane (PM) as discrete punctae and is secreted outside of the cells. Immunogold labeling of sections cut from high-pressure frozen samples reveal EXPO to be spherical double membrane structures resembling autophagosomes. However, unlike autophagosomes, EXPOs are not induced by starvation and do not fuse with the lytic compartment or with endosomes. Instead, they fuse with the PM, releasing a single membrane vesicle into the cell wall. EXPOs are also found in other cell types, including root tips, root hair cells, and pollen grains. EXPOs therefore represent a form of unconventional secretion unique to plants.
Long‐term effects on sward composition and animal performance of reducing fertilizer inputs to upland permanent pasture
Authors: Yu Y.‐W. , Fraser M. D. , Evans J. G. 
Published: December 2010

AbstractThis study investigated the long‐term effects on sward composition and animal performance of applying different fertilizer regimes to upland permanent pasture. The experiment, which was carried out in 2008, was based on a set of replicated (n = 3) plots that had been established in 1990. The effects of applying (i) N, P, K and lime, (ii) P and K plus lime and (iii) lime only were compared with a treatment that received no nutrient applications. Using a put‐and‐take stocking system, the plots were grazed to a target sward surface height of 4 cm by ewes and lambs from April to early August and by ewes only from August to mid‐October. The long‐term reduction in nutrient inputs had led to decreases in the percentages of both sown and unsown grass species within the sward (P < 0·05), and an increase in the percentage of mosses and litter (P < 0·05), with a corresponding reduction in nutritional value. Although there were no statistically significant treatment‐related differences in lamb growth rates, lower fertilizer inputs were associated with a marked decline in stock carrying capacity and associated overall productivity during both the pre‐ and post‐weaning periods (P < 0·001). The findings highlight the challenges faced when attempting to reconcile production and environmental objectives in upland systems.
Cultivation with Untransfected Fibroblasts Stimulates Proliferation of a Single Gene‐Modified Fibroblast Derived from a Clawn Miniature Swine Foetus
Authors: Sato M , Yoshida M , Miyoshi K , Ohtsuka M , Watanabe S 
Published: December 2010

ContentsPorcine embryonic fibroblasts (PEFs) have been used extensively as donor nuclei for the production of cloned pigs via somatic cell nuclear transfer (SCNT). Somatic cell nuclear transfer of gene‐targeted PEFs has been the only way to produce gene‐targeted pigs, given the lack of germ‐line‐competent porcine embryonic stem cells. Unlike other primary‐cultured cells, such as murine embryonic fibroblasts, a single porcine PEF is unable to proliferate under normal conditions in which a certain number of PEFs (likely over 100) can grow normally. This limitation greatly hampers re‐cloning of gene‐modified PEFs, which is required for SCNT. Herein, we demonstrate the cultivation of a single PEF transfectant carrying the pEGFP‐N1 plasmid with intact normal PEFs (>100) in a Terasaki microtest plate, which resulted in stimulation of the growth of the former cell (doubling time = 2.6 days). In contrast, when a single cell was cultured, it could typically divide only once and never divided more than twice. When a single transfectant was seeded in a well of a 96‐well plate together with 5 × 104 untransfected PEFs and was subsequently selected in the presence of G418, we obtained a pure cell population of single‐cell origin. Thus, this method should be useful for the purification of target recombinant pig clones from mosaic populations that cannot be cultured as a single cell or for which suitable cell growth‐promoting conditions are unclear.
Effects of Season and Superovulatory Treatment on Embryo Yields in Fine‐Wool Merinos Maintained Under Field Conditions
Authors: Cueto MI , Gibbons AE , Pereyra‐Bonnet F , Silvestre P , González‐Bulnes A 
Published: December 2010

ContentsThe aim of the study was to assess the effects of superovulatory treatment (multiple FSH‐dose vs single‐shot FSH treatment) and seasonality on embryo yields in fine‐wool Merino ewes. Treatment based on multiple FSH‐dose consisted of 200 mg of FSH (Folltropin®) administered in seven decreasing doses. Single‐shot treatment consisted of a single dose of 70 mg of FSH + eCG. In ewes treated with multiple FSH doses, number of recovered embryos was higher (6.0 ± 0.5 vs 3.5 ± 1.0), while non‐fertilization rate was lower (12.8 ± 3.9 vs 40.3 ± 9.5) during the breeding season when compared to the non‐breeding season (p < 0.05); although similar values of recovered Grades 1–2 embryos were observed between seasons. During the breeding season, proportion of responding ewes (98.1 vs 57.1%), ovulation rate (13.9 ± 0.8 vs 3.2 ± 1.2), recovered structures (7.9 ± 0.6 vs 1.7 ± 0.7), total recovered embryos (6.0 ± 0.5 vs 1.2 ± 0.6) and good‐quality embryos (5.1 ± 0.5 vs 0.9 ± 0.6) were higher for the multiple FSH‐dose treatment than for the single‐shot protocol. In a similar way, in the non‐breeding season, ovulation rate (11.3 ± 1.8 vs 6.0 ± 1.1) and recovered structures (6.6 ± 1.2 vs 2.7 ± 0.6) were higher for the multiple FSH injections protocol than those for the single‐shot treatment, resulting in higher recovered Grades 1–2 embryos (3.2 ± 0.9 vs 1.4 ± 0.5). Current results indicate that seasonal anestrus affected embryo yields when applying multiple FSH‐dose superovulatory treatment in Merino ewes, by decreasing the number of recovered embryos although the number of recovered good‐quality embryos was not affected. During both seasons, multiple FSH injections produced higher ovarian response and number of viable embryos than the single‐shot treatment.
The Role of Oocyte‐Secreted Factors GDF9 and BMP15 in Follicular Development and Oogenesis
Authors: Paulini Fernanda , Melo Eduardo O. 
Published: December 2010

ContentsOvarian physiology is controlled by endocrine and paracrine signals, and the transforming growth factor β (TGFβ) superfamily has a pivotal role in this control. The Bone morphogenetic protein 15 (BMP15) and Growth differentiation factor 9 (GDF9) genes are relevant members of the TGFβ superfamily that encode proteins secreted by the oocytes into the ovarian follicles. Through a paracrine signalling pathway, these factors induce the follicular somatic cells to undergo mitosis and differentiation during follicular development. These events are controlled by a mutually dependent and coordinated fashion during the formation of the granulosa cell layers. Many studies have contributed to our knowledge concerning the paracrine factors acting within the follicular environment, especially regarding GDF9 and BMP15. We aimed to review the relevant contributions of these two genes to animal reproductive physiology.