bluuebunny/crossref_metadata_2025_split huggingface dataset:
phiBIOTICS: catalogue of therapeutic enzybiotics, relevant research studies and practical applications
Authors: Hojckova Katarina , Stano Matej , Klucar Lubos 
Published: March 2013

Abstract

Background
The incidence of bacterial infections in humans along with the growing problem of antibiotic resistance is a major public health concern worldwide. Therefore it is necessary to develop novel therapeutic agents to control microbial pathogens. In this regard, enzybiotics, lytic enzymes endowed with the capacity to degrade bacterial cell wall, are a very promising group of alternative antimicrobials.

Description
Numerous experimental studies have confirmed unique therapeutic capabilities of enzybiotics and hence they are worth of wider attention of the medical community. In order to summarize the state of current knowledge of enzybiotics, we have developed phiBIOTICS, an information portal about known and studied therapeutic enzybiotics. phiBIOTICS contains information on chemical and biological properties of enzybiotics together with compendium of facts retrieved from research studies, where enzybiotics were applied. Our auxiliary phiBiScan program utility is dedicated for prediction of novel potential enzybiotics.

Conclusions
phiBIOTICS presents a solid body of knowledge about all studied therapeutic enzybiotics to date. The database brings high-value information on outcomes of applied research and pre-clinical trials of these prospective antimicrobial agents. This information which was scattered in research papers with heterogeneous quality and relevance is now available in the form of manually curated database. phiBIOTICS and phiBiScan are freely accessible at http://www.phibiotics.org/.
Preoperative serum C- reactive protein: a prognostic marker in patients with upper urinary tract urothelial carcinoma
Authors: Stein Barbara , Schrader Andres Jan , Wegener Gerd , Seidel Christoph , Kuczyk Markus A , Steffens Sandra 
Published: March 2013

Abstract

Background
To analyse the prognostic significance of preoperative C-reactive protein (CRP) serum level in patients with upper urinary tract urothelial carcinoma (UUT-UC).

Methods
We evaluated 158 UUT-UC patients who had undergone surgery in the University Hospital of Hannover (MHH). 143 (89.4%) suffered from cancer in the renal pelvis, 13 (8.1%) patients presented with tumour located in the ureter. A preoperative CRP value was available for 115 patients. The mean (median) follow-up for these patients was 28.3 (15.1) months.

Results
The median (mean) CRP value of all evaluable patients was 10.0 (40.7) mg/l. The CRP-level, stratified into two subgroups (CRP ≤5 vs. >5 mg/l), correlated significantly with muscle invasive tumour stage (36.4 vs. 78.9%; p<0.001), the risk of presenting nodal disease (4.5 vs. 26.8%; p=0.002) and distant metastasis (2.3 vs. 16.9%; p<0.016). The Kaplan-Meier 5-year cancer specific survival (CSS) rates were 54.2 and 26.4% for patients with preoperative CRP levels ≤ and >5 mg/l, respectively (p<0.006). Next to age and the presence of metastasis, multivariate analysis also identified CRP as a continuous variable as an independent prognosticator for CSS.

Conclusions
A high preoperative serum CRP level is associated with locally advanced and metastatic disease in patients with UUT-UC. Its routine use could allow better risk stratification and risk-adjusted follow-up of UUT-UC patients.
Multicenter phase II study of weekly docetaxel, cisplatin, and S-1 (TPS) induction chemotherapy for locally advanced squamous cell cancer of the head and neck
Authors: Bae Woo Kyun , Hwang Jun Eul , Shim Hyun Jeong , Cho Sang Hee , Lee Ki Hyeong , Han Hye Suk , Song Eun-Kee , Yun Hwan Jung , Cho In Sung , Lee Joon Kyoo , Lim Sang-Chul , Chung Woong-Ki , Chung Ik-Joo 
Published: March 2013

Abstract

Background
The purpose of this study was to evaluate the efficacy and tolerability of weekly docetaxel, cisplatin, and S-1 (weekly TPS) as induction chemotherapy for patients with locally advanced head and neck squamous cell carcinoma (HNSCC).

Methods
A total of 35 patients with previously untreated, locally advanced HNSCC were enrolled. Seven patients (20%) were diagnosed with stage III HNSCC and 28 patients (80%) were diagnosed with stage IV. Induction treatment included 30 mg/m2 docetaxel on day 1 and 8, 60 mg/m2 cisplatin on day 1, and 70 mg/m2 S-1 on days 1 to 14. The regimen was repeated every 21 days. After three courses of induction chemotherapy, patients received concurrent chemoradiotherapy.

Results
Among the 35 patients, 30 (85.7%) completed induction chemotherapy. The response to induction chemotherapy was as follows: nine patients (25.7%) achieved a complete response (CR) and the overall response rate (ORR) was 85.7%. Grades 3–4 toxicity during induction therapy included neutropenia (28.5%), neutropenic fever (8.5%), and diarrhea (17.1%). After completion of concurrent chemoradiotherapy, the CR rate was 62.8% and the partial response (PR) was 22.8%. Estimates of progression-free and overall survival at 2 years were 73.2% and 79.3%, respectively.

Conclusions
Weekly TPS is a promising regimen that is well-tolerated, causes minimal myelosuppression and is effective as an outpatient regimen for locally advanced HNSCC.

Trial registration
ClinicalTrials.gov: NCT01645748
Cloud-based active content collaboration platform using multimedia processing
Authors: Han Byong John , Jung In-Yong , Kim Ki-Hyun , Lee Do-kwang , Rho Seungmin , Jeong Chang-sung 
Published: March 2013

Abstract
In this article, a new content-centric collaboration platform called active content collaboration platform which supports automated content-centric collaboration on cloud system is presented. It supports event-driven automatic collaboration by specifying each active work based on active work description language and automating the execution of collaborative task flow composed of active works. It supports a modularized and extensible architecture by making its components in separate modules. Also, it provides a scalable high-performance architecture by supporting multi-level active work processing in active work execution engine, and allocating virtual machines for the computation intensive high-level action such as volume rendering through auto-scalable allocation on cloud system. For the experiment and evaluation, we shall show the results of implementing the collaborative medical application on our system where computation intensive application like a volume rendering is used for MRI analysis.
The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5
Authors: Kropinski Andrew M , Waddell Tom , Meng Juncai , Franklin Kristyn , Ackermann Hans-Wolfgang , Ahmed Rafiq , Mazzocco Amanda , Yates John , Lingohr Erika J , Johnson Roger P 
Published: March 2013

Abstract

Background
Bacteriophages (phages) have been used extensively as analytical tools to type bacterial cultures and recently for control of zoonotic foodborne pathogens in foods and in animal reservoirs.

Methods
We examined the host range, morphology, genome and proteome of the lytic E. coli O157 phage rV5, derived from phage V5, which is a member of an Escherichia coli O157:H7 phage typing set.

Results
Phage rV5 is a member of the Myoviridae family possessing an icosahedral head of 91 nm between opposite apices. The extended tail measures 121 x 17 nm and has a sheath of 44 x 20 nm and a 7 nm-wide core in the contracted state. It possesses a 137,947 bp genome (43.6 mol%GC) which encodes 233 ORFs and six tRNAs. Until recently this virus appeared to be phylogenetically isolated with almost 70% of its gene products ORFans. rV5 is closely related to coliphages Delta and vB-EcoM-FY3, and more distantly related to Salmonella phages PVP-SE1 and SSE-121, Cronobacter sakazakii phage vB_CsaM_GAP31, and coliphages phAPEC8 and phi92. A complete shotgun proteomic analysis was carried out on rV5, extending what had been gleaned from the genomic analyses. Host range studies revealed that rV5 is active against several other E. coli.
Attenuation of HIV-1 replication in macrophages by cannabinoid receptor 2 agonists
Authors: Ramirez Servio H , Reichenbach Nancy L , Fan Shongshan , Rom Slava , Merkel Steven F , Wang Xu , Ho Wen-zhe , Persidsky Yuri 
Published: March 2013

Abstract
CB2 expression is upregulated in HIV-1 infected macrophages; CB2 agonists limits infection by inhibition of the HIV-1-LTR.
Infiltrating monocytes and macrophages play a crucial role in the progression of HIV-1 infection in the CNS. Previous studies showed that activation of the CB2 can attenuate inflammatory responses and affect HIV-1 infectivity in T cells and microglia. Here, we report that CB2 agonists can also act as immunomodulators on HIV-1-infected macrophages. First, our findings indicated the presence of elevated levels of CB2 expression on monocytes/macrophages in perivascular cuffs of postmortem HIV-1 encephalitic cases. In vitro analysis by FACS of primary human monocytes revealed a step-wise increase in CB2 surface expression in monocytes, MDMs, and HIV-1-infected MDMs. We next tested the notion that up-regulation of CB2 may allow for the use of synthetic CB2 agonist to limit HIV-1 infection. Two commercially available CB2 agonists, JWH133 and GP1a, and a resorcinol-based CB2 agonist, O-1966, were evaluated. Results from measurements of HIV-1 RT activity in the culture media of 7 day-infected cells showed a significant decrease in RT activity when the CB2 agonist was present. Furthermore, CB2 activation also partially inhibited the expression of HIV-1 pol. CB2 agonists did not modulate surface expression of CXCR4 or CCR5 detected by FACS. We speculate that these findings indicate that prevention of viral entry is not a central mechanism for CB2-mediated suppression in viral replication. However, CB2 may affect the HIV-1 replication machinery. Results from a single-round infection with the pseudotyped virus revealed a marked decrease in HIV-1 LTR activation by the CB2 ligands. Together, these results indicate that CB2 may offer a means to limit HIV-1 infection in macrophages.
Lactating Ctcgrp Nulls Lose Twice the Normal Bone Mineral Content due to Fewer Osteoblasts and More Osteoclasts, Whereas Bone Mass Is Fully Restored After Weaning in Association With Up-Regulation of Wnt Signaling and Other Novel Genes
Authors: Collins Jillian N. , Kirby Beth J. , Woodrow Janine P. , Gagel Robert F. , Rosen Clifford J. , Sims Natalie A. , Kovacs Christopher S. 
Published: March 2013

AbstractThe maternal skeleton resorbs during lactation to provide calcium to milk and the lost mineral content is restored after weaning. The changes are particularly marked in Ctcgrp null mice, which lose 50% of spine mineral content during lactation but restore it fully. The known calciotropic hormones are not required for skeletal recovery to occur; therefore, unknown factors that stimulate bone formation may be responsible. We hypothesized that the genes responsible for regulating postweaning bone formation are differentially regulated in bone or marrow, and this regulation may be more marked in Ctcgrp null mice. We confirmed that Ctcgrp null mice had twice as many osteoclasts and 30–40% fewer osteoblasts as compared with wild-type mice during lactation but no deficit in osteoblast numbers after weaning. Genome-wide microarray analyses on tibial RNA showed differential expression of 729 genes in wild-type mice at day 7 after weaning vs prepregnancy, whereas the same comparison in Ctcgrp null mice revealed only 283 genes. Down-regulation of Wnt family inhibitors, Sost and Dkk1, and inhibition of Mef2c, a sclerostin stimulator, were observed. Ctsk, a gene expressed during osteoclast differentiation, and Igfbp2, which stimulates bone resorption, were inhibited. Differential regulation of genes involved in energy use was compatible with a net increase in bone formation. The most marked changes occurred in genes not previously associated with bone metabolism. In conclusion, the postlactation skeleton shows dynamic activity with more than 700 genes differentially expressed. Some of these genes are likely to promote bone formation during postweaning by stimulating the proliferation and activity of osteoblasts, inhibiting osteoclasts, and increasing energy use.
Antiproliferative, Antiinvasive, and Proapoptotic Activity of Folate Receptor α-Targeted Liposomal Doxorubicin in Nonfunctional Pituitary Adenoma Cells
Authors: Liu Xiaohai , Ma Sihai , Dai Congxin , Cai Feng , Yao Yong , Yang Yakun , Feng Ming , Deng Kan , Li Guiling , Ma Wenbing , Xin Bing , Lian Wei , Xiang Guangya , Zhang Bo , Wang Renzhi 
Published: March 2013

Abstract
There is an urgent need for novel therapeutic strategies for the treatment of nonfunctional pituitary adenomas (NFPAs), especially those that are invasive. The folate receptor (FR)α is overexpressed in several cancers, including NFPA. The aim of this study was to determine the efficacy of FRα-targeted liposomes loaded with doxorubicin (F-L-DOX) in the treatment of NFPA. We evaluated targeting, cytotoxicity, antiinvasive, and proapoptotic activity of F-L-DOX in 25 primary cell lines derived from patients with NFPAs. We found that these liposomes effectively targeted NFPA cells through FRα and that endocytosis of the liposomes was blocked by 1mM free folic acid. F-L-DOX inhibited proliferation of NFPA cells and promoted apoptosis through activation of caspase-8, caspase-9, and caspase-3/7 more effectively than L-DOX. Furthermore, F-L-DOX also exerted greater antiinvasive ability in NFPA cells than L-DOX through suppression of the secretion of matrix metalloproteinase-2 and matrix metalloproteinase-9. Addition of 1mM free folic acid significantly reduced the pleotropic effects of F-L-DOX in NFPA cells, suggesting that FRα plays a critical role in mediating the antitumor effect of F-L-DOX. Our findings warrant further investigation of F-L-DOX as an alternative therapeutic strategy for the treatment of NFPAs that express FRα.
Randomized Clinical Trial of Vitamin D3 Doses on Prostatic Vitamin D Metabolite Levels and Ki67 Labeling in Prostate Cancer Patients
Authors: Wagner Dennis , Trudel Dominique , Van der Kwast Theodorus , Nonn Larisa , Giangreco Angeline Antonio , Li Doris , Dias Andre , Cardoza Monique , Laszlo Sanda , Hersey Karen , Klotz Laurence , Finelli Antonio , Fleshner Neil , Vieth Reinhold 
Published: March 2013

Context:
Vitamin D3 might benefit prostate cancer (PCa) patients because prostate cells can locally synthesize the active hormone calcitriol.

Objective:
Our objective was to determine the effects of oral vitamin D3 on vitamin D metabolites and PCa proliferative activity in prostate tissue.

Design and Setting:
We conducted a double-blind randomized clinical trial at surgical oncology clinics in Toronto, Canada.

Patients:
PCa patients (Gleason 6 or 7) participated in the study. Of 66 subjects who were enrolled, 63 completed the dosing protocol.

Intervention:
Vitamin D3 (400, 10 000, or 40 000 IU/d) was orally administered before radical prostatectomy.

Main Outcome Measures:
We evaluated vitamin D metabolite levels and Ki67 labeling in surgical prostate tissue. Safety measures, PTH, and prostate-specific antigen (PSA) were also assessed.

Results:
Prostate tissue and serum levels of vitamin D metabolites, including calcitriol, increased dose dependently (P &lt; .03) and were significantly higher in the 40 000-IU/d group than in every other dose group (P &lt; .03). Prostate vitamin D metabolites correlated positively with serum levels (P &lt; .0001). Ki67 measures did not differ significantly among vitamin D dose groups. However, cross-sectional analysis indicated that the calcitriol level attained in prostate was inversely associated with Ki67 intensity and Ki67 (3+) percent positive nuclei in PCa and benign tissue (P &lt; .05). Safety measures did not change adversely with dosing. Compared with the 400-IU/d group, serum PTH and PSA were lower in the combined higher-dose groups at the end of the study (P &lt; .02).

Conclusions:
Oral vitamin D3 raised prostate calcitriol levels (level 1 evidence) and modestly lowered both PSA and PTH. Although Ki67 expression did not differ among dose groups, its levels correlated inversely with prostate calcitriol. These suggestions of clinical benefit justify continued clinical research.
Fischer–Tropsch Synthesis Conducted in Volcanic Reservoir Stone, An Important Factor Caused a Reversed Pattern of Carbon Isotopic for Natural Gases Developed in Deep Layers, Songliao Basin North East China
Authors: Mi Jingkui , Zhang Shuichang , He Kun , Mao Rong 
Published: March 2013

Two types of experiments of source rocks pyrolysis with volcanic reservoir rock and without one were conducted under hydrothermal condition and at 200 °C in gold tube system. The experiments result shows that there is a higher concentration of hydrocarbon gases generated in the experiment with rhyolite of reservoir stone and water than that with only water. Moreover, the hydrocarbon gases generated by experiments with rhyolite show a full reserved pattern of carbon isotope. This indicated that the FST reaction could happened between source rocks and volcanic reservoir rock at relatively low temperature. The numerical calculation for the carbon isotope of the gases from mixture between the gases from our FTS experiments and the typical organic hydrocarbon gases from deep layers of Songliao basin show that the contamination of a little FTS gas (<5%, v/v) could cause the carbon isotope composition of thermal gases great variation. So, Fischer–Tropsch synthesis conducted in volcanic reservoir stone is an un-negligible factor caused the reversed pattern of carbon isotopic for natural gases developed in deep layers, Songliao Basin. This also indicated that the natural gases in deep layers of the basin are organic origin chiefly.
Theoretical Derivation and Application Research of Stepped Horizontal Well Patterns with Coupling Reservoir/Wellbore Flow in Multilayer Reservoir
Authors: Ni Jun , Ren Zhanli , Wang Xiangzeng , Zhan Zhuanying 
Published: March 2013

It is quite difficult to apply the regular well patterns into the development of oilfields due to a series of factors like the geology complexity, the limitation of development cost and the operability in real reservoir. Therefore, a new kind of well pattern is proposed to deal with the above problem. This method focuses on developing multilayer reservoir by the stepped horizontal well, which is deployed with two vertical injectors at both sides, respectively. According to the newly established well pattern, the corresponding productivity formula for the stepped horizontal is deduced. In this process, the stepped horizontal well is divided into several sections by each layer in the first. Secondly, the productivity equation of one section among them is derived on the basis of conformal transformation and potential flow theory, the other section is dealt with in the same way. Thirdly, the simultaneous equations of productivity for each section are solved on the basis of nodal analysis. Besides, the pressure drop loss of wellbore flow in the horizontal section is also taken into consideration. Finally, the total productivity is worked out. In order to prove the applicability of the established productivity formula for the proposed well pattern, the data of well Z12-33 in Zhaozhou oilfield are adopted to calculate the total productivity, the results indicate that the error between calculated value and real production is small, which proves the reliability of this formula. Therefore, this formula can be applied into the real reservoirs to aid the oilfields development.
Individuals with Intellectual Disability Can Self-Teach in Reading
Authors: Loveall Susan J. , Conners Frances A. 
Published: March 2013

Abstract
Previous research has suggested that individuals with intellectual disability (ID) underperform in several areas of reading compared to mental age–matched peers. However, it is unclear how they compare on orthographic aspects of reading, which have to do with learning and matching the specific letter patterns in words. The leading approach to understanding orthographic learning is the self-teaching hypothesis, which suggests that orthographic learning is acquired through the experience of phonologically recoding words. The present study was a first test of the self-teaching hypothesis for individuals with ID in comparison to a group of typically developing children matched on verbal mental age. Results indicated that both groups were able to self-teach.
Validating Functional Measures of Physical Ability for Aging People with Intellectual Developmental Disability
Authors: Maring Joyce R. , Costello Ellen , Birkmeier Marisa C. , Richards Maggie , Alexander Lisa M. 
Published: March 2013

Abstract
Unlike the aging population without intellectual and developmental disabilities (IDD), few standardized performance measures exist to assess physical function and risk for adverse outcomes such as nonfatal, unintentional injuries. We modified 3 selected standardized performance tools in the areas of general fitness (2-Minute Walk Test), balance and gait (Performance-Oriented Mobility Assessment I), and functional independence (Modified Barthel Index) for administration with people with IDD. The modified tools were piloted with 30 participants. Results indicated the measures are strongly associated and successfully distinguished between participants with an adverse health event in the previous year. The modified tools have potential to provide clinicians with quantitative measures that track physical performance changes associated with aging in people with IDD.
Rate of convergence of the density estimation of regression residual
Authors: Györfi László , Walk Harro 
Published: March 2013

Abstract
Consider the regression problem with a response variable Y and with a d-dimensional feature vector X. For the regression function m(x) = E{Y|X = x}, this paper investigates methods for estimating the density of the residual Y − m(X) from independent and identically distributed data. If the density is twice differentiable and has compact support then we bound the rate of convergence of the kernel density estimate. It turns out that for d ≤ 3 and for partitioning regression estimates, the regression estimation error has no influence on the rate of convergence of the density estimate.