A tutorial on information retrieval: basic terms and concepts

This informal tutorial is intended for investigators and students who would like to understand the workings of information retrieval systems, including the most frequently used search engines: PubMed and Google. Having a basic knowledge of the terms and concepts of information retrieval should improve the efficiency and productivity of searches. As well, this knowledge is needed in order to follow current research efforts in biomedical information retrieval and text mining that are developing new systems not only for finding documents on a given topic, but extracting and integrating knowledge across documents

Improve the effectiveness of the opinion retrieval and opinion polarity classification

Opinion retrieval is a document retrieving and ranking process. A relevant document must be relevant to the query and contain opinions toward the query. Opinion polarity classification is an extension of opinion retrieval. It classifies the retrieved document as positive, negative or mixed, according to the overall polarity of the query relevant opinions in the document. This paper (1) proposes several new techniques that help improve the effectiveness of an existing opinion retrieval system; (2) presents a novel two-stage model to solve the opinion polarity classification problem. In this model, every query relevant opinionated sentence in a document retrieved by our opinion retrieval system is classified as positive or negative respectively by a SVM classifier. Then a second classifier determines the overall opinion polarity of the document. Experimental results show that both the opinion retrieval system with the proposed opinion retrieval techniques and the polarity classification model outperformed the best reported systems respectively. Categories and Subject Descriptors H.3.3 [Information Storage and Retrieval]: Information Searc

Multiple Evidence Combination in Image retrieval: Diogenes Searches for People on the Web

Abstract In this work, we examine evidence combination mechAnisms for classifying multimedia information. In particular, we examine linear and Dempster-Shafer methods of evidence combination in the context of identifying personal images on the World Wide Web. An automatic web search engine named Diogenes 1 searches the web for personal images and combines different pieces of evidence for identification. The sources of evidence consist of input from face detection/recognition and text/HTML analysis modules. A degree of uncertainty is involved with both of these sources. Diogenes automatically determines the uncertainty locally for each retrieval and uses this information to set a relative significance for each evidence. To our knowledge, Diogenes is the first image search engine using Dempster-Shafer evidence combination based on automatic object recognition and dynamic local uncertainty assessment. In our experiments Diogenes comfortably outperformed some well known commercial and research prototype image search engines for celebrity image queries

Resonant behaviour in double charge exchange reaction of \pi^+ mesons on the nuclear photoemulsion

The invariant mass spectra of the $pp\pi^-$ and $pp$ systems produced in the double charge exchange (DCX) of positively charged pions on photoemulsion are analysed. A pronounced peak is observed in the $pp\pi^-$ invariant mass spectrum, while the $M_{pp}$ spectrum exhibits a strong Migdal-Watson effect of the proton-proton final state interaction. These findings are in favor of the $NN$-decoupled $NN\pi$ pseudoscalar resonance with T=0 called $d'$.Comment: 13 pages, 5 figures, revised versio

Rule-based deduplication of article records from bibliographic databases

We recently designed and deployed a metasearch engine, Metta, that sends queries and retrieves search results from five leading biomedical databases: PubMed, EMBASE, CINAHL, PsycINFO and the Cochrane Central Register of Controlled Trials. Because many articles are indexed in more than one of these databases, it is desirable to deduplicate the retrieved article records. This is not a trivial problem because data fields contain a lot of missing and erroneous entries, and because certain types of information are recorded differently (and inconsistently) in the different databases. The present report describes our rule-based method for deduplicating article records across databases and includes an open-source script module that can be deployed freely. Metta was designed to satisfy the particular needs of people who are writing systematic reviews in evidence-based medicine. These users want the highest possible recall in retrieval, so it is important to err on the side of not deduplicating any records that refer to distinct articles, and it is important to perform deduplication online in real time. Our deduplication module is designed with these constraints in mind. Articles that share the same publication year are compared sequentially on parameters including PubMed ID number, digital object identifier, journal name, article title and author list, using text approximation techniques. In a review of Metta searches carried out by public users, we found that the deduplication module was more effective at identifying duplicates than EndNote without making any erroneous assignments

Pbx loss in cranial neural crest, unlike in epithelium, results in cleft palate only and a broader midface.

Orofacial clefting represents the most common craniofacial birth defect. Cleft lip with or without cleft palate (CL/P) is genetically distinct from cleft palate only (CPO). Numerous transcription factors (TFs) regulate normal development of the midface, comprising the premaxilla, maxilla and palatine bones, through control of basic cellular behaviors. Within the Pbx family of genes encoding Three Amino-acid Loop Extension (TALE) homeodomain-containing TFs, we previously established that in the mouse, Pbx1 plays a preeminent role in midfacial morphogenesis, and Pbx2 and Pbx3 execute collaborative functions in domains of coexpression. We also reported that Pbx1 loss from cephalic epithelial domains, on a Pbx2- or Pbx3-deficient background, results in CL/P via disruption of a regulatory network that controls apoptosis at the seam of frontonasal and maxillary process fusion. Conversely, Pbx1 loss in cranial neural crest cell (CNCC)-derived mesenchyme on a Pbx2-deficient background results in CPO, a phenotype not yet characterized. In this study, we provide in-depth analysis of PBX1 and PBX2 protein localization from early stages of midfacial morphogenesis throughout development of the secondary palate. We further establish CNCC-specific roles of PBX TFs and describe the developmental abnormalities resulting from their loss in the murine embryonic secondary palate. Additionally, we compare and contrast the phenotypes arising from PBX1 loss in CNCC with those caused by its loss in the epithelium and show that CNCC-specific Pbx1 deletion affects only later secondary palate morphogenesis. Moreover, CNCC mutants exhibit perturbed rostro-caudal organization and broadening of the midfacial complex. Proliferation defects are pronounced in CNCC mutants at gestational day (E)12.5, suggesting altered proliferation of mutant palatal progenitor cells, consistent with roles of PBX factors in maintaining progenitor cell state. Although the craniofacial skeletal abnormalities in CNCC mutants do not result from overt patterning defects, osteogenesis is delayed, underscoring a critical role of PBX factors in CNCC morphogenesis and differentiation. Overall, the characterization of tissue-specific Pbx loss-of-function mouse models with orofacial clefting establishes these strains as unique tools to further dissect the complexities of this congenital craniofacial malformation. This study closely links PBX TALE homeodomain proteins to the variation in maxillary shape and size that occurs in pathological settings and during evolution of midfacial morphology

Length Effects on the Reliability of Dual-Damascene Cu Interconnects

The effects of interconnect length on the reliability of dual-damascene Cu metallization have been investigated. As in Al-based interconnects, the lifetimes of Cu lines increase with decreasing length. However, unlike Al-based interconnects, no critical length exists, below which all Cu lines are âimmortal’. Furthermore, we found multi-modal failure statistics for long lines, suggesting multiple failure mechanisms. Some long Cu interconnect segments have very large lifetimes, whereas in Al segments, lifetimes decrease continuously with increasing line length. It is postulated that the large lifetimes observed in long Cu lines result from liner rupture at the bottom of the vias, which allows continuous flow of Cu between the two bond pads. As a consequence, the average lifetimes of short lines and long lines can be higher than those of lines with intermediate lengths.Singapore-MIT Alliance (SMA

Corrigendum to Comparing Structure-Property Evolution for PM-HIP and Forged Alloy 625 Irradiated with Neutrons to 1dpa [Mater. Sci. Eng. A (2022) 144058]

The authors regret that after publication, they discovered that the dislocation loop number density was undercounted by a factor of 100 for both the PM-HIP and forged specimens. While this does not change the original major conclusions, this necessitates a change in the results presentation (Sections 3.2 and 4.1) and calculated hardening (Table 3, Fig. 5). Corrections to these affected sections are provided in this corrigendum

Highly Sensitive and Cost-Effective Portable Sensor for Early Gastric Carcinoma Diagnosis

Facile and efficient early detection of cancer is a major challenge in healthcare. Herein we developed a novel sensor made from a polycarbonate (PC) membrane with nanopores, followed by sequence-specific Oligo RNA modification for early gastric carcinoma diagnosis. In this design, the gastric cancer antigen CA72-4 is specifically conjugated to the Oligo RNA, thereby inhibiting the electrical current through the PC membrane in a concentration-dependent manner. The device can determine the concentration of cancer antigen CA72-4 in the range from 4 to 14 U/mL, possessing a sensitivity of 7.029 µAU−1mLcm−2 with a linear regression (R2) of 0.965 and a lower detection limit of 4 U/mL. This device has integrated advantages including high specificity and sensitivity and being simple, portable, and cost effective, which collectively enables a giant leap for cancer screening technologies towards clinical use. This is the first report to use RNA aptamers to detect CA72-4 for gastric carcinoma diagnosi