bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polynomial-Time Random Oracles and Separating Complexity Classes
Authors: Hitchcock John M. , Sekoni Adewale , Shafei Hadi 
Published: January 2021

Bennett and Gill [1981] showed that P

A

≠ NP

A

≠ coNP

A

for a random oracle
A
, with probability 1. We investigate whether this result extends to individual polynomial-time random oracles. We consider two notions of random oracles: p-random oracles in the sense of martingales and resource-bounded measure [Lutz 1992; Ambos-Spies et al. 1997], and p-betting-game random oracles using the betting games generalization of resource-bounded measure [Buhrman et al. 2000]. Every p-betting-game random oracle is also p-random; whether the two notions are equivalent is an open problem.

(1) We first show that P

A

≠ NP

A

for every oracle
A
that is p-betting-game random.

Ideally, we would extend (1) to p-random oracles. We show that answering this either way would imply an unrelativized complexity class separation:

(2) If P

A

≠ NP

A

relative to every p-random oracle
A
, then BPP ≠ EXP.

(3) If P

A

≠ NP

A

relative to some p-random oracle
A
, then P ≠ PSPACE.

Rossman, Servedio, and Tan [2015] showed that the polynomial-time hierarchy is infinite relative to a random oracle, solving a longstanding open problem. We consider whether we can extend (1) to show that PH

A

is infinite relative to oracles
A
that are p-betting-game random. Showing that PH

A

separates at even its first level would also imply an unrelativized complexity class separation:

(4) If NP

A

≠ coNP

A

for a p-betting-game measure 1 class of oracles
A
, then NP ≠ EXP.

(5) If PH

A

is infinite relative to every p-random oracle
A
, then PH ≠ EXP.

We also consider random oracles for time versus space, for example:

(6) L

A

≠ P

A

relative to every oracle
A
that is p-betting-game random.
Predictive Value of Tumor Load in Breast Cancer Sentinel Lymph Nodes for Second Echelon Lymph Node Metastases
Authors: van Deurzen C. H. M. , van Hillegersberg R. , Hobbelink M. G. G. , Seldenrijk C. A. , Koelemij R. , van Diest P. J. 
Published: January 2021

Background: The need for routine axillary lymph node dissection (ALND) in patients with invasive breast cancer and low‐volume sentinel node (SN) involvement is questionable. Accurate prediction of second echelon lymph node involvement could identify those patients most likely to benefit from ALND.Methods: A consecutive series of 317 patients with invasive breast cancer and a tumor positive axillary SN followed by ALND was reviewed. Clinicopathologic features of the primary tumor and the SN were assessed as possible predictors of second echelon lymph node involvement.Results: Second echelon metastases were found in 116/317 cases (36.6%). Frequency of second echelon lymph node involvement in patients with isolated tumor cells (ITC, N = 23), micro‐ (N = 101) and macrometastases (N = 193) was 13%, 20% and 48%, respectively (p < 0.001). Based on the area % of SN occupied by tumor no subgroup of patients could be selected with less than 20% second echelon lymph node involvement. However, none of the patients with SN ITC or micrometastases and a primary tumor size ≤1 cm (N = 12, 3.8%) had second echelon lymph node involvement.Conclusions: Accurately measured SN tumor load predicts second echelon lymph node involvement. However, even in patients with ITC, the second echelon lymph nodes are involved in 13% justifying ALND.
Expression of Integrin Alpha10 Is Induced in Malignant Melanoma
Authors: Wenke Ann-Kathrin , Kjellman Christian , Lundgren-Akerlund Evy , Uhlmann Christian , Haass Nikolas K. , Herlyn Meenhard , Bosserhoff Anja K. 
Published: January 2021

Recently, integrin alpha10 was described as a collagen type II‐binding integrin expressed mainly in chondrocytes. However, by array studies we detected integrin alpha10 also to be upregulated in malignant melanoma compared to primary melanocytes. Subsequent analysis of melanoma cell lines and melanoma tumor samples confirmed this finding. Further, we demonstrated that expression of integrin alpha10 is controlled by AP‐2 and Ets‐1, two transcription factors known to be involved in melanoma development and progression. To investigate the functional relevance of integrin alpha10, expression was downregulated via stable antisense transfection. Proliferation assays and colony forming assays revealed no differences comparing antisense integrin alpha10 cell clones with control and wild type melanoma cells, respectively. However, antisense integrin alpha10 cell clones and Mel Im cells treated with an inhibitory antibody against integrin alpha10 showed a reduced migratory potential.In summary, these data indicate that AP‐2 and Ets‐1 regulated expression of integrin alpha10 plays a role in migration of malignant melanoma cells.
Estrogen Receptor Beta Displays Cell Cycle-Dependent Expression and Regulates the G1 Phase through a Non-Genomic Mechanism in Prostate Carcinoma Cells
Authors: Hurtado Antoni , Pinós Tomàs , Barbosa-Desongles Anna , López-Avilés Sandra , Barquinero Jordi , Petriz Jordi , Santamaria-Martínez Albert , Morote Joan , de Torres Inés , Bellmunt Joaquim , Reventós Jaume , Munell Francina 
Published: January 2021

Background: It is well known that estrogens regulate cell cycle progression, but the specific contributions and mechanisms of action of the estrogen receptor beta (ERβ) remain elusive.Methods: We have analyzed the levels of ERβ1 and ERβ2 throughout the cell cycle, as well as the mechanisms of action and the consequences of the over-expression of ERβ1 in the human prostate cancer LNCaP cell line.Results: Both ERβ1 mRNA and protein expression increased from the G1 to the S phase and decreased before entering the G2/M phase, whereas ERβ2 levels decreased during the S phase and increased in the G2/M phase. ERβ1 protein was detected in both the nuclear and non-nuclear fractions, and ERβ2 was found exclusively in the nucleus. Regarding the mechanisms of action, endogenous ERβ was able to activate transcription via ERE during the S phase in a ligand-dependent manner, whereas no changes in AP1 and NFκB transactivation were observed after exposure to estradiol or the specific inhibitor ICI 182,780. Over-expression of either wild type ERβ1 or ERβ1 mutated in the DNA-binding domain caused an arrest in early G1. This arrest was accompanied by the interaction of over-expressed ERβ1 with c-Jun N-terminal protein kinase 1 (JNK1) and a decrease in c-Jun phosphorylation and cyclin D1 expression. The administration of ICI impeded the JNK1–ERβ1 interaction, increased c-Jun phosphorylation and cyclin D1 expression and allowed the cells to progress to late G1, where they became arrested.Conclusions: Our results demonstrate that, in LNCaP prostate cancer cells, both ERβ isoforms are differentially expressed during the cell cycle and that ERβ regulates the G1 phase by a non-genomic mechanism.
Differential Proteomic Analysis of Nuclear Matrix in Muscle‐Invasive Bladder Cancer: Potential to Improve Diagnosis and Prognosis
Authors: Barboro Paola , Rubagotti Alessandra , Orecchia Paola , Spina Bruno , Truini Mauro , Repaci Erica , Carmignani Giorgio , Romagnoli Andrea , Introini Carlo , Boccardo Francesco , Carnemolla Barbara , Balbi Cecilia 
Published: January 2021

Introduction: Although several molecular markers for bladder cancer have been identified, at present little information on prognostic biomarkers is available in the literature. Prognostication of this tumor is largely based on clinicopathological characteristics. Our aim was to identify nuclear matrix (NM) proteins that might serve to better characterize the phenotype of the invasive bladder cancer and to investigate their diagnostic and prognostic roles.Methods: NM proteins expressed in normal (n=3) or non‐tumoral (n=9) tissue specimens and muscle‐invasive bladder cancer (n=21) specimens were analyzed by two dimensional (2D) gel electrophoresis. PDQuest image analysis software was used to generate a comparative NM proteome analysis. Selected spots were characterized by liquid chromatography coupled to tandem mass spectrometry and Western blot.Results: We detected over 800 protein spots in each 2D map and 43 spots were identified. 30 proteins were differentially expressed by bladder tumor cells; among these, 19 proteins were detected in bladder tumoral tissues but not in normal and non‐tumoral tissues and seven proteins correlated with tumor stage. One protein (p54nrb) was strongly correlated with vascular invasions and appeared to be also significantly (P <0.0001) associated with a decreased probability of survival.Conclusion: Important alterations in NM proteins occur in muscle‐invasive bladder cancer. The differentially expressed proteins include biomarkers potentially useful for disease diagnosis, progression and prognosis. Our findings beyond improving the understanding of the biology of bladder cancer, could help to stratify patients into different prognostic subgroups and to select those who might be better candidate to multimodal therapeutic approaches.
Protein Profiling of B‐Cell Lymphomas Using Tissue Biopsies: A Potential Tool for Small Samples in Pathology
Authors: Jansen Corine , Hebeda Konnie M. , Linkels Marianne , Grefte Johanna M. M. , Raemaekers John M. M. , van Krieken Johan H. J. M. , Groenen Patricia J. T. A. 
Published: January 2021

Non‐Hodgkin’s lymphoma comprises many related but distinct diseases and diagnosis and classification is complex. Protein profiling of lymphoma biopsies may be of potential value for use in this lymphoma classification and the discovery of novel markers. In this study, we have optimized a method for SELDI‐TOF MS based protein profiling of frozen tissue sections, without dissection of tumour cells. First we have compared chip surfaces and lysis buffers. Also, we have determined the minimal input using laser dissection microscopy. Subsequently, we have analyzed and compared protein profiles of diffuse large B‐cell lymphoma (n=8), follicular lymphoma (n=8) and mantle cell lymphoma (n=8). Benign, reactive lymph nodes (n=14) were used as a reference group.CM10 chip surface in combination with urea lysis buffer and an input of approximately 50,000 lymphocytes allowed the detection of many differential peaks. Identification of the diffuse large B‐cell lymphoma cases was reliably made in the supervised classification. Unsupervised clustering showed segregation into a benign/indolent cluster predominantly formed by benign, reactive lymph nodes and follicular lymphoma cases and into a more aggressive cluster formed by diffuse large B‐cell lymphoma and mantle cell lymphoma cases. In conclusion, our protocol enables protein profiling of protein lysates derived from small histological samples and the subsequent detection of many differentially expressed proteins, without the need of tumour cell dissection. These results support further evaluation of protein profiling of small lymphoma biopsies as an additional tool in pathology.
Cyclooxygenase-2 Mediated Regulation of E-Cadherin Occurs in Conventional But Not Early-Onset Gastric Cancer Cell Lines
Authors: Sitarz R. , Leguit R. J. , de Leng W. W. J. , Morsink F. H. M. , Polkowski W. P. , Maciejewski R. , Offerhaus G. J. A. , Milne A. N. 
Published: January 2021

Background: COX-2 and E-cadherin, involved in invasion and metastasis, are molecules critical for gastric carcinogenesis. A relationship between them is documented in non-small cell lung and prostate cancer. We present novel evidence of a relationship between COX-2 and E-cadherin expression in gastric cancer.Methods: Using qPCR and Western blots analysis on celecoxib and PGE2 treated and untreated gastric cancer cell lines derived from tumours of the intestinal type (MKN45, MKN28, AGS3, MKN7) and immunohistochemistry of 178 gastric cancers on tissue microarrays (TMA), we examined the COX-2/E-cadherin relationship.Results: Down-regulation of COX-2 by celecoxib led to up-regulation of E-cadherin mRNA and protein levels in conventional gastric cancer cell lines, whereas expression was down regulated in the early-onset gastric cancer (EOGC) cell line. Immunohistochemistry on TMAs of 178 gastric cancers showed no correlation between COX-2 and E-cadherin expression in the conventional or early gastric cancer groups.Conclusions: The results suggest that COX-2 has an impact on transcriptional regulation of E-cadherin in gastric cancer and our findings further highlight the intriguing nature of EOGCs which appear to have a molecular phenotype distinct from conventional gastric cancer. In addition, our findings also suggest that reduction of COX-2 using nonsteroidal anti-inflammatory drugs in gastric cancer chemoprevention may only be relevant for older patients.
Absence of Granzyme B Positive Tumour-Infiltrating Lymphocytes in Primary Melanoma Excisional Biopsies is Strongly Associated with the Presence of Sentinel Lymph Node Metastasis
Authors: van Houdt I. S. , Sluijter B. J. R. , van Leeuwen P. A. M. , Moesbergen L. M. , Hooijberg E. , Meijer C. J. L. M. , de Gruijl T. D. , Oudejans J. J. , Boven E. 
Published: January 2021

Background: Sentinel Lymph Node (SLN) status is strongly related to clinical outcome in melanoma patients. In this study we investigated the possible association between the presence of activated and/or suppressive Tumour Infiltrating Lymphocytes (TILs) and SLN status in clinically stage I/II melanoma patients.Methods: Diagnostic primary melanoma samples from 20 patients with a sentinel lymph node metastasis were compared to melanoma samples from 20 patients with a negative sentinel lymph node, who were matched for gender, age and Breslow thickness. Presence of activated Granzyme B positive (GrB+) TILs, presence of suppressive (FoxP3+) TILs and MHC class I antigen expression on tumour cells were analysed by immunohistochemistry.Results: FoxP3 and MHC-I expression had no direct bearing on the presence of melanoma metastases in the SLN. Whereas the presence of activated GrB+ TILs in the primary melanoma had no predictive value for SLN status either, their absence was strongly associated with the presence of metastasis in the SLN (p=0.001). While both GrB+ and FoxP3+ TILs could be detected in SLN metastases, a majority did not display MHC-I expression.Conclusions: These data support a role for cytotoxic T cells in the prevention of early metastasis of melanoma to the draining lymph nodes.
Potential Biomarkers of Colorectal Adenoma–Dysplasia–Carcinoma Progression: mRNA Expression Profiling and In Situ Protein Detection on TMAs Reveal 15 Sequentially Upregulated and 2 Downregulated Genes
Authors: Galamb Orsolya , Sipos Ferenc , Spisák Sándor , Galamb Barnabás , Krenács Tibor , Valcz Gábor , Tulassay Zsolt , Molnár Béla 
Published: January 2021

Background: As most colorectal cancers (CRC) develop from villous adenomas, studying alterations in gene expression profiles across the colorectal adenoma–dysplasia–carcinoma sequence may yield potential biomarkers of disease progression.Methods: Total RNA was extracted, amplified, and biotinylated from colonic biopsies of 15 patients with CRC, 15 with villous adenoma and 8 normal controls. Gene expression profiles were evaluated using HGU133Plus2.0 microarrays and disease progression associated data were validated with RT-PCR. The potential biomarkers were also tested at the protein level using tissue microarray samples of 103 independent and 16 overlapping patients.Results: 17 genes were validated to show sequentially altered expression at mRNA level through the normal–adenoma–dysplasia–carcinoma progression. Prostaglandin-D2 receptor (PTGDR) and amnionless homolog (AMN) genes revealed gradually decreasing expression while the rest of 15 genes including osteonectin, osteopontin, collagen IV–alpha 1, biglycan, matrix GLAprotein, and von Willebrand factor demonstrated progressively increasing expression. Similar trends of expression were confirmed at protein level for PTGDR, AMN, osteopontin and osteonectin.Conclusion: Downregulated AMN and PTGDR and upregulated osteopontin and osteonectin were found as potential biomarkers of colorectal carcinogenesis and disease progression to be utilized for prospective biopsy screening both at mRNA and protein levels. Gene alterations identified here may also add to our understanding of CRC progression.
Oncogenic K-Ras Activates p38 to Maintain Colorectal Cancer Cell Proliferation during MEK Inhibition
Authors: van Houdt Winan J. , de Bruijn Menno T. , Emmink Benjamin L. , Raats Danielle , Hoogwater Frederik J. H. , Rinkes Inne H. M. Borel , Kranenburg Onno 
Published: January 2021

Background: Colon carcinomas frequently contain activating mutations in the K-ras proto-oncogene. K-ras itself is a poor drug target and drug development efforts have mostly focused on components of the classical Ras-activated MEK/ERK pathway. Here we have studied whether endogenous oncogenic K-ras affects the dependency of colorectal tumor cells on MEK/ERK signaling.Methods: K-ras mutant colorectal tumor cell lines C26, HCT116 and L169 were used. K-ras or components of the MEK/ERK and p38 pathway were suppressed by RNA interference (RNAi). MEK was inhibited by U0126. p38 was inhibited by SB203850.Results: MEK inhibition, or suppression of MEK1/2 or ERK1/2 by RNA interference, reduced the proliferation rate of all colorectal cancer cell lines. However, cell proliferation returned to normal after two weeks of chronic inhibition, despite the continued suppression of MEK or ERK. In contrast, K-ras-suppressed tumor cells entered an irreversible senescent-like state following ERK pathway inhibition. MEK inhibition or ERK1/2 suppression caused activation of p38α in a K-ras-dependent manner. Inhibition or suppression of p38α prevented the recovery of K-ras mutant tumor cells during prolonged MEK inhibition.Conclusions: Oncogenic K-ras activates p38α to maintain cell proliferation during MEK inhibition. MEK-targeting therapeutics can create an acquired tumor cell dependency on p38α.
Gene Promoter Methylation Patterns throughout the Process of Cervical Carcinogenesis
Authors: Yang Nan , Nijhuis Esther R. , Volders Haukeline H. , Eijsink Jasper J. H. , Lendvai Ágnes , Zhang Bo , Hollema Harry , Schuuring Ed , Wisman G. Bea A. , van der Zeea Ate G. J. 
Published: January 2021

Objectives: To determine methylation status of nine genes, previously described to be frequently methylated in cervical cancer, in squamous intraepithelial lesions (SIL).Methods: QMSP was performed in normal cervix, low-grade (L)SIL, high-grade (H)SIL, adenocarcinomas and squamous cell cervical cancers, and in corresponding cervical scrapings.Results: Only CCNA1 was never methylated in normal cervices and rarely in LSILs. All other genes showed methylation in normal cervices, with CALCA, SPARC and RAR-β2 at high levels. Methylation frequency of 6 genes (DAPK, APC, TFPI2, SPARC, CCNA1 and CADM1) increased with severity of the underlying cervical lesion. DAPK showed the highest increase in methylation frequency between LSIL and HSIL (10% vs. 40%, p < 0.05), while CCNA1 and TFPI2 were most prominently methylated in cervical cancers compared to HSILs (25% vs. 52%, p < 0.05, 30% vs. 58%, p < 0.05). CADM1 methylation in cervical cancers was related to depth of invasion (p < 0.05) and lymph vascular space involvement (p < 0.01), suggesting a role in invasive potential of cervical cancers. Methylation ratios in scrapings reflected methylation status of the underlying lesions (p < 0.05).Conclusion: Methylation of previously reported cervical cancer specific genes frequently occurs in normal epithelium. However, frequency of methylation increases during cervical carcinogenesis, with CCNA1 and DAPK as the best markers to distinguish normal/LSIL from HSIL/cancer lesions.
Pre T-Cell Receptor Alpha (pTα) Expression Patterns and Functional Analysis in Human T-Cell Lymphoblastic Leukemia
Authors: Ivanyi Philipp , Morgan Michael , Piao Wenji , Ukena Sya N. , Steube Klaus , Ganser Arnold , Franzke Anke 
Published: January 2021

Background: The pTα/preTCR regulates the β-selection, a crucial T-cell developmental checkpoint, providing a most potent survival advantage to thymocytes mediated by the src-kinase p56Lck.Methods: To define the relevance of pTα in human T-cell lymphoblastic leukemia (T-ALL), we analyzed in T-ALL cell lines (n=14) pTα and p56Lck mRNA and protein expression as also the tyrosine-phosphorylation. The p56Lck specific src-protein-tyrosine kinase inhibitor (PTK-I) PP1 was used in growth inhibition assays. IC50 value determination, cell cycle- and apoptosis analyses were performed in T-ALL-, non-T-ALL- and murine transgenic cell lines.Results: pTα expression patterns were markedly different in T-ALL cell lines as compared to those reported for normal lymphoid counterparts. PP1 induced in 6/11 T-ALL cell lines a survival disadvantage resulting from a cell cycle arrest in the G1/0 phase in thymic lymphoblastic cells and apoptosis induction in the immature cell line HSB-2, respectively. PP1 sensitive cell lines expressed the target protein p56Lck and showed a corresponding P-Tyr signal.Conclusions: Sensitivity of thymic T-ALLs to PP1 clearly underlines the impact of pTα mediated proliferation in this leukemic sub-type. In addition, p56Lck represents also independently of pTα a promising therapeutical target for the src-kinase inhibitors in neoplastic lymphoid diseases.
A Virtual Microscopy System to Scan, Evaluate and Archive Biomarker Enhanced Cervical Cytology Slides
Authors: Grabe Niels , Lahrmann Bernd , Pommerencke Thora , von Knebel Doeberitz Magnus , Reuschenbach Miriam , Wentzensen Nicolas 
Published: January 2021

Background: Although cytological screening for cervical precancers has led to a reduction of cervical cancer incidence worldwide it is a subjective and variable method with low single-test sensitivity. New biomarkers like p16 that specifically highlight abnormal cervical cells can improve cytology performance. Virtual microscopy offers an ideal platform for assisted evaluation and archiving of biomarker-stained slides.Methods: We first performed a quantitative analysis of p16-stained slides digitized with the Hamamatsu NDP slide scanner. From the results an automated algorithm was created to reliably detect cells, nuclei and p16-stained cells. The algorithm's performance was evaluated on two complete slides and tiles from 52 independent slides (11,628, 4094 and 25,619 cells/clusters, respectively).Results: We achieved excellent performance to discriminate unstained cells from nuclei and biomarker-stained cells. The automated algorithm showed a high overall and positive agreement (99.0–99.7% and 70.9–83.4%, respectively) with the gold standard and had a very high sensitivity (89.1–100.0%) and specificity (98.9–100.0%) to detect biomarker-stained cells.Conclusions: We implemented a virtual microscopy system allowing highly efficient automated prescreening and archiving of biomarker-stained slides. Based on the initial results, we will evaluate the performance of our system in large epidemiologic studies against disease endpoints.