bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved Indexing & Searching Throughput
Authors: Crane Matt 
Published: June 2016

Information retrieval is the process of finding relevant information in large corpora of documents based on user queries. Within the discipline there are a number of open research questions and areas. This thesis presents a systematic study into improving the speed of all aspects of an information retrieval system, without such improvements having an adverse effect on the effectiveness of that system.
Several key areas of the indexing process were investigated: the effect of removing spam and correcting encoding errors at indexing time; the amount of parallelism and further improvements to the indexing process; the methods of vocabulary accumulation and collision resolution within a hash table; and as part of the indexing process, a new family of hash functions for information retrieval which exploit the properties of natural language was proposed.
Search performance was also investigated by examining the effects of the spam removal on search quality. A relationship between the size of a collection and the pre-calculation of retrieval scores was discovered.
Overall results indicate a 30% improvement of indexing throughput. This is accompanied by a 15% increase in search quality, whilst its speed could be increased by 25% without degrading quality. The pre-calculation of retrieval scores further improves retrieval speed by up to 3--.
These results were compared against other open-source indexing systems by ATIRE when participating in the SIGIR 2015 RIGOR Workshop Reproducibility Challenge. The results of this challenge show that ATIRE is the fastest indexing system (taking half the time of the next best system), and the second fastest search system using the discovered relationship.
Engaged or Frustrated?
Authors: Edwards Ashlee 
Published: June 2016

One of the primary ways researchers have characterized engagement is by an increase in search actions. Another possibility is that instead of experiencing increased engagement, people who click and query frequently are actually frustrated; several studies have shown that frustration is also characterized by increases in clicking and querying behaviors. This research seeks to illuminate the differences in search behavior between participants who are engaged and frustrated, as well as investigate the effect of task interest on engagement and frustration. To accomplish this, a laboratory experiment was conducted with 40 participants. Participants completed four tasks, and responded to questionnaires that measured their engagement, frustration, and stress. Participants were asked to rank eight topics based on interest, and were given their two most interesting and two least interesting tasks. Poor search result quality was introduced to induce frustration during their most interesting and least interesting tasks.
This study found that physiological signals hold some promise for disambiguating engagement and frustration, but this depends on the time frame and manner in which they are examined. Frustrated participants had significantly more skin conductance responses during the task, while engaged participants had greater increases in skin conductance during the first 60 seconds of the task. Significant main and interaction effects for interest and frustration were found for heart rate in the window analysis, indicating that heart rate fluctuations over time can be most effective in distinguishing engagement from frustration. The multilevel modeling of engagement and frustration confirmed this, showing that interest contributed significantly to the model of skin conductance, while frustration contributed significantly to the model of heart rate.
This study also found that interest had a significant effect on engagement, while the frustrator effectively created frustration. Frustration also had a significant effect on selfreported stress. Participants exhibited increases in search actions such as clicks and scrolls during periods of both engagement and frustration, but a regression analyses showed that scrolls, clicks on documents, and SERP clicks were most predictive of a frustrating episode. A significant main effect for interest was found for time between queries, indicating that this could be a useful signal of engagement. A model including the physiological signals and search behaviors showed that physiological signals aided in the prediction of engagement and frustration.
Findings of this research have provided insight into the utility of physiological signals in distinguishing emotional states as well as provided evidence about the relationship among search actions, engagement and frustration. These findings have also increased our understanding of the role emotions play in search behavior and how information about a searcher's emotional state can be used to improve the search experience.
Extending Faceted Search to the Open-Domain Web
Authors: Kong Weize 
Published: June 2016

Faceted search enables users to navigate a multi-dimensional information space by combining keyword search with drill-down options in each facets. For example, when searching "computer monitor" in an e-commerce site, users can select brands and monitor types from the the provided facets {"Samsung", "Dell", "Acer", ...} and {"LET-Lit", "LCD", "OLED",...}. It has been used successfully for many vertical applications, including e-commerce and digital libraries. However, this idea is not well explored for general web search in an opendomain setting, even though it holds great potential for assisting multi-faceted queries and exploratory search.
The goal of this work is to explore this potential by extending faceted search into the opendomain web setting, which we call Faceted Web Search. We address three fundamental issues in Faceted Web Search, namely: how to automatically generate facets (facet generation); how to re-organize search results with users' selections on facets (facet feedback); and how to evaluate generated facets and entire Faceted Web Search systems.
In conventional faceted search, facets are generated in advance for an entire corpus either manually or semi-automatically, and then recommended for particular queries in most of the previous work. However, this approach is difficult to extend to the entire web due to the web's large and heterogeneous nature. We instead propose a query-dependent approach, which extracts facets for queries from their web search results. We further improve our facet generation model under a more practical scenario, where users care more about precision of presented facets than recall.
The dominant facet feedback method in conventional faceted search is Boolean filtering, which filters search results by users' selections on facets. However, our investigation shows Boolean filtering is too strict when extended to the open-domain setting. Thus, we propose soft ranking models for Faceted Web Search, which expand original queries with users' selections on facets to re-rank search results. Our experiments show that the soft ranking models are more effective than Boolean filtering models for Faceted Web Search.
To evaluate Faceted Web Search, we propose both intrinsic evaluation, which evaluates facet generation on its own, and extrinsic evaluation, which evaluates an entire Faceted Web Search system by its utility in assisting search clarification. We also design a method for building reusable test collections for such evaluations. Our experiments show that using the Faceted Web Search interface can significantly improve the original ranking if allowed sufficient time for user feedback on facets.
Immuno-PET Imaging of Engineered Human T Cells in Tumors
Authors: Mall Sabine , Yusufi Nahid , Wagner Ricarda , Klar Richard , Bianchi Henrique , Steiger Katja , Straub Melanie , Audehm Stefan , Laitinen Iina , Aichler Michaela , Peschel Christian , Ziegler Sibylle , Mustafa Mona , Schwaiger Markus , D'Alessandria Calogero , Krackhardt Angela M. 
Published: June 2016

AbstractSensitive in vivo imaging technologies applicable to the clinical setting are still lacking for adoptive T-cell–based immunotherapies, an important gap to fill if mechanisms of tumor rejection or escape are to be understood. Here, we propose a highly sensitive imaging technology to track human TCR-transgenic T cells in vivo by directly targeting the murinized constant TCR beta domain (TCRmu) with a zirconium-89 (89Zr)-labeled anti–TCRmu-F(ab')2 fragment. Binding of the labeled or unlabeled F(ab')2 fragment did not impair functionality of transgenic T cells in vitro and in vivo. Using a murine xenograft model of human myeloid sarcoma, we monitored by Immuno-PET imaging human central memory T cells (TCM), which were transgenic for a myeloid peroxidase (MPO)–specific TCR. Diverse T-cell distribution patterns were detected by PET/CT imaging, depending on the tumor size and rejection phase. Results were confirmed by IHC and semiquantitative evaluation of T-cell infiltration within the tumor corresponding to the PET/CT images. Overall, these findings offer a preclinical proof of concept for an imaging approach that is readily tractable for clinical translation. Cancer Res; 76(14); 4113–23. ©2016 AACR.
A Strong B-cell Response Is Part of the Immune Landscape in Human High-Grade Serous Ovarian Metastases
Authors: Montfort Anne , Pearce Oliver , Maniati Eleni , Vincent Benjamin G. , Bixby Lisa , Böhm Steffen , Dowe Thomas , Wilkes Edmund H. , Chakravarty Probir , Thompson Richard , Topping Joanne , Cutillas Pedro R. , Lockley Michelle , Serody Jonathan S. , Capasso Melania , Balkwill Frances R. 
Published: June 2016

Abstract
Purpose: In high-grade serous ovarian cancer (HGSOC), higher densities of both B cells and the CD8+ T-cell infiltrate were associated with a better prognosis. However, the precise role of B cells in the antitumor response remains unknown. As peritoneal metastases are often responsible for relapse, our aim was to characterize the role of B cells in the antitumor immune response in HGSOC metastases.
Experimental Design: Unmatched pre and post-chemotherapy HGSOC metastases were studied. B-cell localization was assessed by immunostaining. Their cytokines and chemokines were measured by a multiplex assay, and their phenotype was assessed by flow cytometry. Further in vitro and in vivo assays highlighted the role of B cells and plasma cell IgGs in the development of cytotoxic responses and dendritic cell activation.
Results: B cells mainly infiltrated lymphoid structures in the stroma of HGSOC metastases. There was a strong B-cell memory response directed at a restricted repertoire of antigens and production of tumor-specific IgGs by plasma cells. These responses were enhanced by chemotherapy. Interestingly, transcript levels of CD20 correlated with markers of immune cytolytic responses and immune complexes with tumor-derived IgGs stimulated the expression of the costimulatory molecule CD86 on antigen-presenting cells. A positive role for B cells in the antitumor response was also supported by B-cell depletion in a syngeneic mouse model of peritoneal metastasis.
Conclusions: Our data showed that B cells infiltrating HGSOC omental metastases support the development of an antitumor response. Clin Cancer Res; 23(1); 250–62. ©2016 AACR.
Tumor-Derived CCL2 Mediates Resistance to Radiotherapy in Pancreatic Ductal Adenocarcinoma
Authors: Kalbasi Anusha , Komar Chad , Tooker Graham M. , Liu Mingen , Lee Jae W. , Gladney Whitney L. , Ben-Josef Edgar , Beatty Gregory L. 
Published: June 2016

Abstract
Purpose: Local tumor growth is a major cause of morbidity and mortality in nearly 30% of patients with pancreatic ductal adenocarcinoma (PDAC). Radiotherapy is commonly used for local disease control in PDAC, but its efficacy is limited. We studied the impact of selectively intervening on radiotherapy-induced inflammation as an approach to overcome resistance to radiotherapy in PDAC.
Experimental Design: PDAC cell lines derived from primary pancreatic tumors arising spontaneously in KrasLSL-G12D/+;Trp53LSL-R172H/+;Pdx-1 Cre mice were implanted into syngeneic mice and tumors were focally irradiated using the Small Animal Radiation Research Platform (SARRP). We determined the impact of depleting T cells and Ly6C+ monocytes as well as inhibiting the chemokine CCL2 on radiotherapy efficacy. Tumors were analyzed by flow cytometry and IHC to detect changes in leukocyte infiltration, tumor viability, and vascularity. Assays were performed on tumor tissues to detect cytokines and gene expression.
Results: Ablative radiotherapy alone had minimal impact on PDAC growth but led to a significant increase in CCL2 production by tumor cells and recruitment of Ly6C+CCR2+ monocytes. A neutralizing anti-CCL2 antibody selectively inhibited radiotherapy-dependent recruitment of monocytes/macrophages and delayed tumor growth but only in combination with radiotherapy (P &lt; 0.001). This antitumor effect was associated with decreased tumor proliferation and vascularity. Genetic deletion of CCL2 in PDAC cells also improved radiotherapy efficacy.
Conclusions: PDAC responds to radiotherapy by producing CCL2, which recruits Ly6C+CCR2+ monocytes to support tumor proliferation and neovascularization after radiotherapy. Disrupting the CCL2–CCR2 axis in combination with radiotherapy holds promise for improving radiotherapy efficacy in PDAC. Clin Cancer Res; 23(1); 137–48. ©2016 AACR.
Distinct Transcriptional Changes and Epithelial–Stromal Interactions Are Altered in Early-Stage Colon Cancer Development
Authors: Mo Allen , Jackson Stephen , Varma Kamini , Carpino Alan , Giardina Charles , Devers Thomas J. , Rosenberg Daniel W. 
Published: June 2016

Abstract
Although the progression of mutated colonic cells is dependent upon interactions between the initiated epithelium and surrounding stroma, the nature of these interactions is poorly understood. Here, the development of an ultrasensitive laser capture microdissection (LCM)/RNA-seq approach for studying the epithelial and stromal compartments of aberrant crypt foci (ACF) is described. ACF are the earliest identifiable preneoplastic lesion found within the human colon and are detected using high-definition endoscopy with contrast dye spray. The current analysis focused on the epithelium of ACF with somatic mutations to either KRAS, BRAF, or APC, and expression patterns compared with normal mucosa from each patient. By comparing gene expression patterns among groups, an increase in a number of proinflammatory NF-κB target genes was identified that was specific to ACF epithelium, including TIMP1, RELA, and RELB. Distinct transcriptional changes associated with each somatic mutation were observed and a subset of ACF display BRAFV600E-mediated senescence-associated transcriptome characterized by increased expression of CDKN2A. Finally, LCM-captured ACF-associated stroma was found to be transcriptionally distinct from normal-appearing stroma, with an upregulation of genes related to immune cell infiltration and fibroblast activation. Immunofluorescence confirmed increased CD3+ T cells within the stromal microenvironment of ACF and an abundance of activated fibroblasts. Collectively, these results provide new insight into the cellular interplay that occurs at the earliest stages of colonic neoplasia, highlighting the important role of NF-κB, activated stromal fibroblasts, and lymphocyte infiltration.
Implications: Fibroblasts and immune cells in the stromal microenvironment play an important role during the earliest stages of colon carcinogenesis. Mol Cancer Res; 14(9); 795–804. ©2016 AACR.
Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia
Authors: Trinquand Amélie , dos Santos Nuno R. , Tran Quang Christine , Rocchetti Francesca , Zaniboni Benedetta , Belhocine Mohamed , Da Costa de Jesus Cindy , Lhermitte Ludovic , Tesio Melania , Dussiot Michael , Cosset François-Loïc , Verhoeyen Els , Pflumio Françoise , Ifrah Norbert , Dombret Hervé , Spicuglia Salvatore , Chatenoud Lucienne , Gross David-Alexandre , Hermine Olivier , Macintyre Elizabeth , Ghysdael Jacques , Asnafi Vahid 
Published: June 2016

AbstractCancer onset and progression involves the accumulation of multiple oncogenic hits, which are thought to dominate or bypass the physiologic regulatory mechanisms in tissue development and homeostasis. We demonstrate in T-cell acute lymphoblastic leukemia (T-ALL) that, irrespective of the complex oncogenic abnormalities underlying tumor progression, experimentally induced, persistent T-cell receptor (TCR) signaling has antileukemic properties and enforces a molecular program resembling thymic negative selection, a major developmental event in normal T-cell development. Using mouse models of T-ALL, we show that induction of TCR signaling by high-affinity self-peptide/MHC or treatment with monoclonal antibodies to the CD3ϵ chain (anti-CD3) causes massive leukemic cell death. Importantly, anti-CD3 treatment hampered leukemogenesis in mice transplanted with either mouse- or patient-derived T-ALLs. These data provide a strong rationale for targeted therapy based on anti-CD3 treatment of patients with TCR-expressing T-ALL and demonstrate that endogenous developmental checkpoint pathways are amenable to therapeutic intervention in cancer cells.Significance: T-ALLs are aggressive malignant lymphoid proliferations of T-cell precursors characterized by high relapse rates and poor prognosis, calling for the search for novel therapeutic options. Here, we report that the lineage-specific TCR/CD3 developmental checkpoint controlling cell death in normal T-cell progenitors remains switchable to induce massive tumor cell apoptosis in T-ALL and is amenable to preclinical therapeutic intervention. Cancer Discov; 6(9); 972–85. ©2016 AACR.See related commentary by Lemonnier and Mak, p. 946.This article is highlighted in the In This Issue feature, p. 932
Tumor- and Neoantigen-Reactive T-cell Receptors Can Be Identified Based on Their Frequency in Fresh Tumor
Authors: Pasetto Anna , Gros Alena , Robbins Paul F. , Deniger Drew C. , Prickett Todd D. , Matus-Nicodemos Rodrigo , Douek Daniel C. , Howie Bryan , Robins Harlan , Parkhurst Maria R. , Gartner Jared , Trebska-McGowan Katarzyna , Crystal Jessica S. , Rosenberg Steven A. 
Published: June 2016

Abstract
Adoptive transfer of T cells with engineered T-cell receptor (TCR) genes that target tumor-specific antigens can mediate cancer regression. Accumulating evidence suggests that the clinical success of many immunotherapies is mediated by T cells targeting mutated neoantigens unique to the patient. We hypothesized that the most frequent TCR clonotypes infiltrating the tumor were reactive against tumor antigens. To test this hypothesis, we developed a multistep strategy that involved TCRB deep sequencing of the CD8+PD-1+ T-cell subset, matching of TCRA–TCRB pairs by pairSEQ and single-cell RT-PCR, followed by testing of the TCRs for tumor-antigen specificity. Analysis of 12 fresh metastatic melanomas revealed that in 11 samples, up to 5 tumor-reactive TCRs were present in the 5 most frequently occurring clonotypes, which included reactivity against neoantigens. These data show the feasibility of developing a rapid, personalized TCR-gene therapy approach that targets the unique set of antigens presented by the autologous tumor without the need to identify their immunologic reactivity. Cancer Immunol Res; 4(9); 734–43. ©2016 AACR.
Synthesis and Implementation (In STM8S) of Phased Circular Antenna Arrays Using Taguchi Method
Authors: Nemri Nadhem , Badri Hani Wadie , Ghayoula Ridha , Trabelsi Hichem , Gharsallah Ali 
Published: June 2016

<span lang="EN-US">This paper is aimed at assessing the effectiveness of the phase-only control strategy based on a customized Taguchi method when applied to Uniform Circular Arrays (UCA). The objective of this paper consists to contribute the main lobe optimization of the smart antenna using Taguchi's method. We used the cited method in order to determine phase's weights for each element of the circular antenna array in order to steer the principal lobe from -65° to 65° covering all angular space. After that, we made an electronic platform using the microcontroller STM8S in order to implement an intelligent system. The architecture of this work had used a digital phase shifters, a demodulator AD8347, a modulator AD8349, an array antenna, cards STM8S-Discovery.</span>
Elevated Angiopoietin-2 Level in Patients With Continuous-Flow Left Ventricular Assist Devices Leads to Altered Angiogenesis and Is Associated With Higher Nonsurgical Bleeding
Authors: Tabit Corey E. , Chen Phetcharat , Kim Gene H. , Fedson Savitri E. , Sayer Gabriel , Coplan Mitchell J. , Jeevanandam Valluvan , Uriel Nir , Liao James K. 
Published: June 2016

Background:
Nonsurgical bleeding is the most common adverse event in patients with continuous-flow left ventricular assist devices (LVADs) and is caused by arteriovenous malformations. We hypothesized that deregulation of an angiogenic factor, angiopoietin-2 (Ang-2), in patients with LVADs leads to increased angiogenesis and higher nonsurgical bleeding.

Methods:
Ang-2 and thrombin levels were measured by ELISA and Western blotting, respectively, in blood samples from 101 patients with heart failure, LVAD, or orthotopic heart transplantation. Ang-2 expression in endothelial biopsy was quantified by immunofluorescence. Angiogenesis was determined by in vitro tube formation from serum from each patient with or without Ang-2–blocking antibody. Ang-2 gene expression was measured by reverse transcription–polymerase chain reaction in endothelial cells incubated with plasma from each patient with or without the thrombin receptor blocker vorapaxar.

Results:

Compared with patients with heart failure or those with orthotopic heart transplantation, serum levels and endothelial expression of Ang-2 were higher in LVAD patients (
P
=0.001 and
P
<0.001, respectively). This corresponded to an increased angiogenic potential of serum from patients with LVADs (
P
<0.001), which was normalized with Ang-2 blockade. Furthermore, plasma from LVAD patients contained higher amounts of thrombin (
P
=0.003), which was associated with activation of the contact coagulation system. Plasma from LVAD patients induced more Ang-2 gene expression in endothelial cells (
P
<0.001), which was reduced with thrombin receptor blockade (
P
=0.013). LVAD patients with Ang-2 levels above the mean (12.32 ng/mL) had more nonsurgical bleeding events compared with patients with Ang-2 levels below the mean (
P
=0.003).

Conclusions:
Our findings indicate that thrombin-induced Ang-2 expression in LVAD patients leads to increased angiogenesis in vitro and may be associated with higher nonsurgical bleeding events. Ang-2 therefore may contribute to arteriovenous malformation formation and subsequent bleeding in LVAD patients.