Negative Concord Research Articles

Rapid detection of the SARS-CoV-2 omicron variants based on high-resolution melting curve analysis.

With the continuous spread of the SARS-CoV-2 globally, viral mutations have accumulated. As a result, SARS-CoV-2 became more contagious, and has a higher risk of immune escape and reinfection. To identify variants and have an awareness of the prevalence of these variants, this study selected four segments containing mutations on the S gene of the SARS-CoV-2. Then a rapid and convenient variants detection method was established using high-resolution melting(HRM) analysis combined with nested polymerase chain reaction(PCR). The total detection process takes about 5h. Through comprehensive analysis of the results from the four reaction systems, the identification of seven important Omicron variants(BA.2, BA.2.75, BA.5.2, BF.7, BQ.1, XBB.1 and XBB.2) can be achieved, with significant differentiation in the melting curves of each variant group. The method established in this study was used to genotype positive specimens in COVID-19 nucleic acid testing, the overall concordance rate compared to whole genome sequencing results was 88.9%, and the positive concordance rate of each sublineage was greater than 80% and the negative concordance rate was greater than 94.4%. The detection of clinical specimens has demonstrated that the HRM analysis established in this study is an effective, rapid and convenient variant identification method, which can be used for monitoring SARS-CoV-2 variants and has important value in addressing public health issues caused by the ongoing mutations of the SARS-CoV-2.

Negative concord by phase: multiple downward agree and the parametrization of edge features

Abstract We divorce Negative Concord (NC) among two or more n-items, which is invariably present in Romance languages, from the mutual exclusion or cooccurrence between clausal negation markers (CNMs) and other n-items. The standard minimalist treatment in terms of Agree with respect to a formal feature [n] (for [negation]) is maintained here. However, an EPP-like principle, conceived as a (parametrized) condition regulating the representation of [n] at phase edges is introduced to deal with CNMs. By divorcing the n-EPP condition from n-Agree, we eliminate Zeijlstra’s Upward Agree in favor of Multiple Downward Agree between a phase head probe endowed with Formal Feature FF and one or more elements endowed with the same interpretable feature FF in the WorkSpace. We argue that these theoretical moves are beneficial from an empirical point of view. Focusing on varieties spoken in Northern Italy, we argue that an exhaustive typology of Romance negative systems can be derived by the parametrized [n]-EPP. We claim that the present approach allows this variation to be accounted for within the syntax – specifically, no recourse is made to semantic variation.

Negative Dependencies in Turkish

In this paper, we provide an overview of negative dependencies in Turkish. The first are elements such as hiçkimse, which sometimes seem to mean ‘anybody’ and sometimes ‘nobody’. We argue that unlike a standard Negative Polarity Item (NPI) like English anybody, these items should be analyzed as neg-words licensed under Negative Concord (NC). We also discuss further properties of these items, including whether they are universals or existentials. The second set of items that display a negative dependency are universal quantifiers such as herkes ‘everybody’. Unlike their counterparts in many languages, these items obligatorily scope under negation, which raises the question of why a universal is sensitive to negation in the way it is. We account for this behavior in terms of negative polarity sensitivity based on a referentiality requirement we dub the Non-Entailment-of-Non-Existence Condition, following a particular analysis of a class of NPIs in Mandarin. The final case of negative dependency we evaluate is modals that have to scope under or above negation. These cases constitute instances of polarity sensitivity in English and beyond, especially clearly in the case of modal PPIs. We show that in Turkish, however, they do not, and the apparent negative dependency follows from the syntax of Tense-aspect-modality (TAM) morphology.

Development of a Lateral Flow Strip-Based Recombinase-Aided Amplification for Active Streptococcus dysgalactiae emerging in channel catfish (Ictalurus punctatus)

Streptococcus dysgalactiae has become an important pathogen affecting mammals and fish (especially farmed fish). The development of a rapid, accurate, and sensitive diagnostic method will aid in the prevention of S. dysgalactiae infection. In this study, a method combining recombinase-aided amplification and a lateral flow dipstick (RAA-LFD) was developed to detect active S. dysgalactiae infection. The RAA-LFD detection was based on the ISP gene of S. dysgalactiae as the target, which could be accomplished with the lowest detection limit of 1.002×102 pg/μL reaction under optimal reaction conditions of 39 °C for 15 min. RAA-LFD and conventional PCR were used to detect 50 experimental samples invaded by S. dysgalactiae disease materials. The results showed that the positive concordance rate of the two methods was 97.6%, the negative concordance rate was 90.0%, and the total concordance rate was 98.0%. Compared with conventional PCR, the Area Under the ROC Curve (AUC) of RAA-LFD was 0.950, and the sensitivity and specificity were 100% and 90%, respectively. The RAA-LFD of S. dysgalactiae infection is convenient for rapid clinical detection.

A-301 Evaluation of Second-Generation Visby Medical Sexual Health Point-of-Care Test: Clinical Concordance, Analytical Error Rates, and Result Turnaround Time

Abstract Background Rapid testing for Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis may be useful for antibiotic stewardship initiatives. Our institution recently implemented the second-generation Visby Medical Sexual Health Test (Visby Gen2) for rapid diagnosis of STIs in our emergency department. Here we (1) compared result concordance of the (Visby Gen2) to the first-generation Visby Medical Sexual Health Click Test (Visby Gen1), (2) compared assay failure rates of the Visby Gen1 to Gen2 tests, and (3) compared result turnaround time (TAT) for clinically ordered rapid STI tests to central laboratory STI results. Methods Accuracy was assessed using residual clinical samples in Aptima buffer submitted for routine molecular STI testing (C. trachomatis, N. gonorrhoeae, and T. vaginalis) in the central laboratory on the Panther platform (Hologic). Aptima samples were diluted 1:33 in Visby collection buffer prior to testing on the Visby cartridge. Clinically reported results were used as reference results. Diluted samples with discordant results were re-tested on the reference method and the result from the dilution was used in calculations. Assay failure rates were calculated as the number of failed assays compared to the total assays performed. TAT for rapid and central lab testing was calculated as time of sample received in laboratory to time verified in laboratory information system. Results For Visby Gen1 we observed negative concordance of 100% (41/41) for C. trachomatis, 97.5% (39/40) for N. gonorrhoeae, and 97.1% (34/35) for T. vaginalis. Positive concordance was 91.7% (11/12) for C. trachomatis, 100% (11/11) for N. gonorrhoeae, and 100% (17/17) for T. vaginalis. For Visby Gen1 we observed a 10.5% (12/114) cartridge failure rate. For Visby Gen2, we observed negative concordance of 100% (59/59) for C. trachomatis, 100% (63/63) for N. gonorrhoeae, and 100% (55/55) for T. vaginalis while positive concordance was 100% (10/10) for C. trachomatis, 100% (6/6) for N. gonorrhoeae, and 90.9% (10/11) for T. vaginalis. The Visby Gen2 assay displayed a 4.9% (4/81) cartridge failure rate. Six weeks after implementing the Visby Gen2 assay in our ED, rapid STI panel TAT was 0.48 hours on average (n=20). In the central laboratory the average TAT was 22.31 hours (n=7892). Conclusions Assay concordance to reference method was similar for Visby Gen1 and Gen2 assays. The cartridge failure rate improved by 46.7% with the Gen2 assay which should decrease the need to repeat testing due to assay failure. Result TAT decreased by 97.8% when comparing rapid Visby results to central laboratory. Therefore, Visby STI testing using the Gen2 assay can provide accuracy and rapid results likely to facilitate more rapid patient management.

Comparison of Abbot ID Now Method with Eurobioplex RT-PCR SARS-Cov-2 Multiplex Method for Detection of SARS-Cov-2 from Nasopharyngeal and Oropharyngeal Samples

Background: COVID 19 created an urgent demand for rapid diagnosis to encircle this pandemic and improve patient management. In this context, we evaluated the concordance of the ID NOW test compared to the Eurobioplex RT-PCR test in the rapid diagnosis of SARS-CoV-2. Methods: To evaluate the concordance of the assay at different viral loads, 154 positive samples were selected to represent the full range of Ct values observed on the Eurobioplex RT-PCR assay, ranging from 14 to 38 cycles. Positive concordance for the ID Now assay was calculating dusing Eurobioplex RT-PCR as the reference test. An additional 70 negative samples were selected to assess negative concordance. Results: Compared to Eurobioplex RT-PCR, the overall positive agreement was 79% with ID Now. Negative agreement was 100% for ID Now. ID Now showed 100% positive agreement for medium and high viral concentrations (Ct value <30). However, for Ct values >30, the positive agreement was 33.3% for ID Now. Conclusions: This study shows a major limitation of ID Now for specimens collected in universal transport media with lower viral concentrations. Further studies are necessary to evaluate the performance of ID Now for dry nasopharyngeal swabs (manufacturer's recommended method).

Detection of egg white allergy in children by specific IgE microarray chemiluminescence immunoassay

BackgroundAllergen testing has emerged as a pivotal component in prevention and treatment strategies for allergic diseases among children and the utilization of specific IgE (sIgE) through a fully automated chemiluminescent microarray immunoassay (CLMIA) has emerged as a promising trend in the simultaneous detection of multiple allergenic components of children. MethodsThe accuracy and reliability of CLMIA were verified using children’s serum samples that concentrated on allergens. the allergens. The clinical diagnostic practicability of CLMIA was assessed through comprehensive evaluations including measurements of the limit of detection (LOD), intra-batch, and inter-batch precision, linearity analysis, the cross-contamination rate, and the concordance rate with the Phadia system. ResultsAfter the optimization process of CLMIA, the LODs for allergens were calculated to be below 0.01 kU/L, demonstrating the high sensitivity of CLMIA. All components exhibited good linearity within the range of 0.1–100.0 kU/L and the coefficient of determinations (R2 > 0.99). The data of intra-batch precision (<10 %) and inter-batch data (<15 %) illustrated the high reproducibility of CLMIA. The cross-contamination rates for allergens (<0.5 %) showed the high accuracy of CLMIA without interfering. The positive concordance rate between CLMIA and the Phadia system exceeds 90 % with a good negative concordance rate (>85 %) and the Kappa coefficients (>0.8), suggesting the close alignment of CLMIA and the Phadia system and showing the satisfactory clinical potential of CLMIA in children’s allergy disease. ConclusionsThe application of CLMIA has been promising in allergen testing, especially for detecting multiple allergenic components in children.

Utilidad del PCR múltiplex de hemocultivo para el diagnóstico microbiológico de infecciones nosocomiales del sistema nervioso central en pacientes críticos

Background and objectiveTo determine the usefulness of a molecular biology technique for nucleic acid amplification using real-time polymerase chain reaction (PCR) originally designed for microbiological diagnosis in blood cultures, when applied to cerebrospinal fluid (CSF) samples. Materials and methodsRetrospective, observational, single-center study, carried out between January 2017 and February 2024 in a 28-bed multipurpose critical care unit. All patients with suspected postneurosurgical infection and CSF cytochemical alterations were included. In addition to the microbiological study of the CSF by traditional methods, the BioFire® Blood Culture Identification2 (BCID) panel was applied directly to CSF samples. Traditional culture methods were considered as the reference standard for microbiological identification. The main variable of interest was the percentage of concordance of microbial identification between traditional cultures and BCID. Results29 patients were included. The diagnosis of central nervous system infection was confirmed in 14 cases (48.2%), 7 post-neurosurgical meningitis, 6 infections associated with ventriculostomy and 1subdural empyema. The most frequently found microorganisms were Acinetobacter baumannii and Klebsiella pneumoniae. No discordances were found between PCR and cultures, so both the positive (14/14) and negative identification concordance (15/15) were 100% between both methods. ConclusionsIn patients with suspected post-neurosurgical infection and compatible CSF alterations, multiplex PCR blood cultures applied directly to CSF samples could be considered a useful and accurate tool for rapid microbiological diagnosis in infections of the central nervous system.

A register approach to negative concord versus negative polarity items in English

Abstract Negative concord (NC) is used in many English varieties but usually considered ungrammatical in ‘standard’ contemporary English, where negative polarity items (NPIs) are used. In this paper, we take a novel experimental approach to the use of NC versus NPI constructions, in relation to register, sets of speech repertoires linked to specific situational and functional parameters. We report on two rating experiments with American and British English participants using interlocutor relations as a formality manipulation. Results show that (i) across both samples, NC constructions were rated as less appropriate than NPI associates, and (ii) there was a register effect in the American English data in that NC was rated less appropriate in formal than informal contexts. Our study is the first to provide experimental evidence for the register-sensitivity of NC constructions in American English.

Evaluation of the FPMC respiratory panel for detection of respiratory tract pathogens in nasopharyngeal swab and sputum specimens

ObjectivesThe performance of the new Respiratory Pathogen panel (fluorescent probe melting curve, FPMC) for the qualitative detection of 12 organisms (chlamydia pneumoniae, mycoplasma pneumoniae, adenovirus, influenza A virus, influenza B virus, parainfluenza virus, rhinovirus, etc.) was assessed.MethodsProspectively collected nasopharyngeal swab (NPS) and sputum specimens (n = 635) were detected by using the FPMC panel, with the Sanger sequencing method as the comparative method.ResultsThe overall percent concordance between the FPMC analysis method and the Sanger sequencing method was 100% and 99.66% for NPS and sputum specimens, respectively. The FPMC testified an overall positive percent concordance of 100% for both NPS and sputum specimens. The FPMC analysis method also testified an overall negative percent concordance of 100% and 99.38% for NPS and sputum specimens, respectively.ConclusionsThe FPMC analysis method is a stable and accurate assay for rapid, comprehensive detecting for respiratory pathogens.

Negative concord in fragments: Reexamining the evidence against the negativity of negation markers

I argue that particular restrictions on the recoverability of elided negation in fragment answers in negative-concord languages follow from the semantics of questions. Drawing parallels with other ellipsis phenomena, I also highlight the role of Agree in making certain heads recoverable. This invalidates a major argument against the analysis of negative-concord items as universal quantifiers scoping above negation.

Comparison of quantitative and qualitative anti-dsDNA assays.

In evaluation of systemic lupus erythematosus (SLE), anti-double-stranded DNA antibodies (anti-dsDNA) play a significant role in diagnosis, monitoring SLE activity, and assessing prognosis. However, evaluations of the performance and limitations for recently developed methods for anti-dsDNA assessment are sparse. Specimens used for antinuclear antibody testing (n = 129) were evaluated for anti-dsDNA assay comparability across 4 medical centers in the United States. The methods compared were Werfen Quanta Lite dsDNA, Zeus Scientific dsDNA Enzyme Immunoassay, Bio-Rad multiplex immunoassay (MIA) dsDNA, ImmunoConcepts Crithidia, and Bio-Rad Laboratories Crithidia. For quantitative anti-dsDNA measurements, Spearman's correlation coefficient was highest between Zeus and Werfen (ρ = 0.86; CI, 0.81-0.90; P < .0001). Comparison of MIA to Werfen or Zeus yielded similar results to each other (ρ = 0.58; CI, 0.44-0.68; P < .0001; and ρ = 0.59; CI, 0.46-0.69; P < .0001, respectively), but lower than the correlation between Zeus and Werfen. Positive concordance between assays ranged from 31.4% to 97.1%, and negative concordance between assays ranged from 58.5% to 100%. The detection of anti-dsDNA in those with SLE diagnosis ranged from 50.9% to 77.4% for quantitative assays and 15.1% to 24.5% for Crithidia assays. Current quantitative anti-dsDNA assays are not interchangeable for patient follow-up. Crithidia-based assays demonstrate high negative concordance and lack positive concordance among the methods.

Styling Authenticity in Country Music

Country music has become commercially successful both in the US and worldwide. It is perceived as a genre that values authenticity, which may be reflected in the choice of linguistic features, with (White) Southern American English (SAE) serving as the “default” variety. Given the recent diversification of the genre, the question arises whether the use of SAE features is still considered obligatory as a kind of “supralocal norm”. This study compared the lyrics of 600 highly successful songs by male and female artists from White Southern, Black Southern, and White non-Southern backgrounds. The aim was to test (i) whether morphosyntactic SAE features are used to index authenticity in the sense of having become enregistered for this music genre and (ii) whether non-Southerners engage in the styling of relevant markers. It emerged that non-Southerners use more of these features than their Southern counterparts, providing preliminary evidence for “genre fitting” as a means of indexing authenticity. However, there is only one marker that qualifies as a core Country feature used across all artist groups, namely negative concord. As this item arguably is better categorized as vernacular universal, SAE morphosyntax appears to have largely lost its indexical function in Country, while accent features are still vital to establishing cultural authenticity.

Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours.

The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA-based sequencing (targeted RNA-seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA-seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA-seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA-seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA-seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH-positive analyses showed a lower percentage of rearrangement-positive nuclei (range 15-41%) compared to the concordant FISH-positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA-seq findings. For the EWSR1 FISH probe, we observed a gene-dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA-seq (22.9%). This study demonstrates an added value of targeted RNA-seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear: NAB2::NCOA2, YAP1::NUTM2B, HSPA8::BRAF, and PDE2A::PLAG1. Overall, targeted RNA-seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.

Reverse Agree Is Not The Only Way To Agree: Evidence From Korean Negative Concord

Reverse Agree Is Not The Only Way To Agree: Evidence From Korean Negative Concord

Establishing the limits between Polarity Sensitivity, Negative Polarity and Negative Concord

Abstract In this paper, by focussing on the behaviour of polarity elements from a variety of languages from different language families (namely, Basque, Hindi, English, Romanian, Spanish, Greek, Czech, and Russian) we investigate the relationship between Polarity Sensitive Items (PSIs) and Negative Polarity Items (NPIs) on the one hand, and between PSIs and Negative Concord items (NCIs) on the other. Based on a number of contrasts that we find, we argue that: (i) if a language has PSIs it does not necessarily have NCIs; (ii) PSIs need to be distinguished from NPIs; (iii) NCIs emerge as a subtype of PSIs, not of NPIs; and (iv) all languages that show Negative Concord (NC) also have Polarity Sensitivity (PS), but the opposite does not hold. We thus postulate that PS is a general phenomenon across languages with Negative Polarity (NPol) and NC as possible subtypes of PS but independent among them, and argue against the standard hypothesis that NC is a special subtype of NPol.

Spanish Negative Concord Items: Experimental Evidence for Their Status as Strict Negative Polarity Items

This study investigates the semantic status of Spanish Negative Concord Items (NCIs) through their comparison with English Negative Quantifiers (NQs) and Polarity Items (PIs) in acceptability judgment tasks conducted among native speakers of Spanish and English. NCIs exhibit a dual behavior depending on their syntactic context, which has resulted in various analyses that categorize them as NQs, PIs, or non-negative indefinites. The findings from this investigation provide experimental confirmation that Spanish NCIs behave like strict Negative Polarity Items (NPIs) or indefinites that are exclusively licensed by a syntactically local anti-veridical operator (i.e., negation). This experimental approach sheds light on the longstanding controversy surrounding the semantic characterization of Spanish NCIs and contributes to our understanding of their behavior across a wide array of linguistic contexts.

Negative PPs and Negative Inversion

This study explores various issues related to negative PPs, focusing on (i) why some negative PPs trigger negative inversion, whereas some do not, (ii) why negative phrases can have scope beyond their c-domain, and (iii) why the distribution of negative PPs is restricted. This study is divided into two parts. The first part demonstrates that negative phrases exhibit a pattern similar to wh-phrases. They cooccur with a zero morpheme NEGø, which carries out the function of extending their restriction. Just as Q extends the restriction of a wh-operator and triggers pied-ping, NEGø extends the restriction of a negative operator, enabling it to have scope beyond its c-domain. The second part argues that English employs covert negative concord in that in negative sentences T must be merged with a covert head called Polarity, which has the feature [u(ninterpretable) Neg]. Additionally, it suggests that (i) the [uNeg]-feature on Polarity can be deleted via a mutual c-command relationship with a NegP, and (ii) when the [uNeg]-feature on it cannot be deleted in situ, it triggers head movement as a last resort. This claim provides a principled account for negative inversion and the distribution of negative PPs.

Clinical usefulness of the “GeneSoC® SARS-CoV-2 N2 Detection Kit”

Abstract Objectives The GeneSoC® that launched recently enables the quantitative detection of target genes (in approximately 15 min) using microfluidic thermal cycling technology. Here, we compared the diagnostic performance of the “GeneSoC® SARS-CoV-2 N2 Detection Kit” (Kyorin assay) and conventional severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection assays to verify the clinical usefulness of the Kyorin assay. Methods Two hundred samples (100 nasopharyngeal and 100 saliva specimens) were collected from patients with suspected SARS-CoV-2 infection between May 2020 and August 2021. Conventional SARS-CoV-2 detection assays were performed using the Japanese National Institute of Infectious Diseases (NIID) assay, Ampdirect™ 2019-nCoV Detection Kit (SHIMADZU assay), and Lumipulse Presto SARS-CoV-2 Ag (FUJIREBIO assay), according to each manufacturer’s instructions. Results Using the NIID and SHIMADZU assays as references, the positive and negative concordance rates and the kappa coefficient in the Kyorin assay were 96.9–97.9 %, 99.0–100.0 %, and 0.96–0.98, respectively. The positivity rate of the FUJIREBIO assay was slightly lower than that of the reference assay (p&lt;0.05). Conclusions The Kyorin assay showed a favorable concordance rate with conventional SARS-CoV-2 detection assays, making it a useful, rapid, and high-performance assay for detecting SARS-CoV-2, which may lead to early diagnosis and appropriate treatment.

West Germanic diachronic constant: the case of negative constructions

This paper explores the common path of the sentence negation practice in the Early West Germanic languages. The prior idea is to find out the general set of markers, which implement the negation pattern. Our assumption is that West Germanic languages, as it has been shown in many papers, contrast with East Germanic and North Germanic languages by ways of negation marking. Our aim is to define the status of the grammatical phenomenon in question within the suggested period. Having assumed that all West Germanic languages may share a similar sentence negation pattern, we laid a special emphasis on their structural characteristics. We also hypothesize that gradual changes of this period were occurring due to the general rearrangement of these language system, which incurred the elimination of the redundant elements. According to Jespersen’s cycle, all the languages under consideration faced multiple negation, i.e., the phenomenon of negative concord (NEG-concord). The latter implies the that preverbal negative particles have been removed from the negation pattern both due to their weakening and the rise of the new supportive element, which originated from the independent structural unit wiht ‘thing’. The rise of the supportive element in the Early West Germanic languages is considered to be a part of the Common Germanic NEG-concord pattern. This lexical-grammatical element turned out to be the one that allowed further eliminating the multiple negation practice in West Germanic languages.