bluuebunny/crossref_metadata_2025_split huggingface dataset:
B-206 Tick-borne disease molecular testing positivity and coinfection incidence in the northeastern united states: 2021-2023
Authors: Pratt G , Matsushita F , Bi C , Rao L V 
Published: October 2024

Abstract

Background
The CDC estimates that Lyme disease affects hundreds of thousands of people each year in the United States. Tick-borne diseases caused by pathogens such as Anaplasma phagocytophilum, Babesia microti, Ehrlichia chaffeensis, and species of Borrelia follow a seasonal pattern due to the life cycle of disease-carrying ticks. In endemic areas, like the northeastern United States, the risk of coinfection by multiple tick-borne disease pathogens is higher and can complicate patient treatment. For example, while Anaplasma and Borrelia can be treated with doxycycline a Babesia coinfection would not be resolved with this medication. In this study, we performed a retrospective analysis of tick-borne disease molecular testing results to monitor positivity rates and incidence of coinfection.

Methods
This retrospective analysis included whole blood specimens submitted to a regional clinical laboratory in the northeastern United States for tick-borne disease molecular testing. Test results from 2021-2023 were analyzed for positivity rate trends and coinfection incidence. DNA was isolated from patient specimens and tested using laboratory developed real-time Taq polymerase PCR assays.

Results
Positivity rates for all tick-borne disease pathogens studied followed typical seasonal patterns (Table). Beginning in the early spring, as nymphs ended their dormancy and began to feed, infection rates of tick-borne disease climbed. Infections peaked in mid-summer and remained elevated through late autumn. For Anaplasma, a biphasic pattern was observed, with a smaller peak in late autumn when adult ticks are most active. Coinfections with Anaplasma and Babesia were observed in 136 specimens, while coinfections with Borrelia and Babesia were observed in 145 specimens.

Conclusions
Positivity rates for tick-borne disease pathogens followed expected seasonal patterns in the northeastern US. The incidence of coinfections involving Babesia microti highlights the importance of properly identifying tick-borne infections given the different treatment regimens indicated.
B-219 Pseudo-exclusion From Paternity due to Maternal Uniparental Disomy of Chromosome 2
Authors: Levi J , Batista J G , Barroso P V , Moratori D , Batistutti V P , Osorio P S , Andrade L M , Rosenberg C 
Published: October 2024

Abstract

Background
Uniparental disomy (UPD) is the abnormal situation in which both members of a chromosome pair exclusively comprise material of one of the parents. The incidence of uniparental disomy (UPD) of any chromosome is estimated in 1:3500 live births; this rare condition may be relevant not only for medical genetics, but also for parental testing.

Methods
We describe a case of trio paternity test using 55 informative STR loci, 30 of these were performed whith GlobalFiler Express KIT - Thermo Fisher (GFE) and Investigator HDPlex - Qiagen (IHDP); capillary electrophoresis using 3500XL - Applied BioSystems; analyses using Genemapper IDX 4.0 - Applied BioSystems. The Y haplotype and 8 additional autosomal STRs were performed by a reference laboratory, which assists us in complex cases. Genotyping with a 1,6 million marker SNP-array (GDA-cyto, Illumina) was analyzed using NxClinical software(Bionano).

Results
Inconsistencies were observed in four loci, namely TPOX, D2S441, D2S1338 and D2S1360. All four markers mapped on chromosome 2 and were compatible with the mother´s genotype, raising the suspicion of a maternal UPD2. SNP-array analyse showed 4 large blocks with absence of heterozygosity on chromosome 2 (AOH - arr[GRCh38] 2p25.3p24.1(10587_22202427)x2 hmz, 2p21p11.2(43674352_90357502)x2 hmz, 2q22.1q31.1(141240699_170583494)x2 hmz, 2q36.3q37.3(227133255_242119896)x2 hmz), comprising a total of 112,9 Mb. No large AOH blocks were observed in any other chromosome.

Conclusions
The results indicate the presence of a UPD2. As the result of an unusually high-number of crossing-overs (n=6), several heterozygous and homozygous blocks were present on chromosome 2 (see figure 1). Rare cases of pseudo-exclusions of either maternity or paternity due to UPD have been reported. Together with the case reported here, they highlight the necessity to consider inconsistencies of markers that map into a single chromosome as likely resulting from UPD.
B-234 Evaluating the diagnostic utility of dd-cf-dna in renal allograft surveillance: a single-center perspective
Authors: Aravamudhan A , Krug K , Stoffel M , Muluhngwi P 
Published: October 2024

Abstract

Background
Donor-derived cell-free DNA (dd-cf-DNA) tests offer a non-invasive alternative to biopsy for allograft surveillance in solid organ transplantation. Unlike biopsies, dd-cf-DNA tests are not subject to interpretation bias and have the potential to detect subclinical rejection, which can lead to graft dysfunction and poor outcomes. At our institution, dd-cf-DNA testing is currently offered as a send out test and we sought to evaluate its efficacy in monitoring our post-transplant patients.

Methods
We retrospectively examined electronic health records of 50 renal transplant patients with dd-cf-DNA (using AlloSure and Prospera assays) between January 1st, 2019, and December 31st, 2022 to assess diagnostic utility of dd-cf-DNA relative to donor-specific antibodies (DSA) and biopsy (all predictors of graft function). Statistical analysis included correlation testing with t-tests.

Results
Overall, dd-cf-DNA levels correlated with DSA levels (p = 0.0002) and patients with both HLA-class I and II DSA had significantly higher dd-cf-DNA levels (p&lt; 0.05). The Prospera dd-cf-DNA assay appeared to be a better predictor of DSA levels (p = 0.04) than the Allosure dd-cf-DNA assay. Though not statistically significant, there was trend towards an increase in dd-cf-DNA in patient with biopsy-proven graft injury and rejection vs no rejection. Interestingly, dd-cf-DNA levels were significantly elevated in patients with biopsy-proven antibody mediated rejection (ABMR). Because dd-cfDNA levels have been reported to be impacted by sensitizing events including prior transplant, we evaluated and observed levels of dd-cf-DNA to be higher in patients with a history of more than one graft vs single graft recipients (p&lt; 0.0001) and this observation was prominent in the Allosure assay.

Conclusions
Our findings suggest that dd-cf-DNA testing holds promise as a valuable tool for graft surveillance and early detection of ABMR. The lack of correlation with biopsy-confirmed rejections may be attributed to the dd-cf-DNA assays’ ability to detect rejection events earlier in the disease progression process compared to biopsy. Time course analysis will be beneficial. Additionally, the observed differences between AlloSure and Prospera emphasize the significance of thoroughly evaluating and selecting assays, particularly in multi-transplant recipients. We highlight that our initial analysis is limited due to a small sample size. However, we aim to assess 200 patients by the conclusion of this study.
B-296 Assessment of Clozapine Assay on The Automated, High-performance Beckman AU Analyzer
Authors: McCormick D , Eubanks C , Walker C , Swartzwelder J , Jones J , Li J 
Published: October 2024

Abstract

Background
Treatment-resistant schizophrenia (TRS) affects approximately one in three patients with schizophrenia. The timely initiation of clozapine therapy is crucial for achieving remission in TRS patients. However, long turnaround times (TATs) associated with sending clozapine tests to reference laboratories cause significant challenges, leading to delays in treatment initiation and compromising patient outcomes. To address this issue, we implemented in-house clozapine testing on Beckman AU analyzers, aiming to facilitate early clozapine initiation and enhance confidence in prescribing and monitoring clozapine therapy for TRS patients.

Methods
The Beckman AU clozapine assay is a homogenous competitive nanoparticle agglutination assay. Precision and linearity were assessed for the Beckman AU DxC700 clozapine assay using manufacturer-provided standards. We conducted a correlation study involving 31 samples analyzed on both Beckman AU DxC 700 and LC-MS/MS methods. Data analysis was performed using Deming and Linear regression methods. Additionally, we analyzed 356 clozapine tests performed in-house on Beckman AU DxC700 between March 15th and Sept 10th, 2023, and compared them with 1399 clozapine tests sent to a reference laboratory using the LC-MS/MS method from March 13th, 2020, to March 13th, 2023. Turnaround time was evaluated.

Results
The Beckman AU DxC700 clozapine assay exhibited excellent performance across the measuring range, with intra-assay and inter-assay coefficients of variation ranging from 1.7-3.6% and 2.2-5.3%, respectively. The assay demonstrated linearity over the five recommended ranges (68-1500 ng/mL) without significant bias observed. The Beckman AU DxC700 and LC-MS/MS clozapine assays displayed excellent correlation (R2=0.948, slope=0.941, intercept=6.3). Implementation of in-house clozapine testing led to a significant reduction in total turnaround time, from 3922 minutes to 116 minutes. The time from sample receipt to results also decreased substantially, from 3894 minutes to 32 minutes.

Conclusions
The clozapine assay was validated and routinely measured in-house using the Beckman AU DxC700 automated assay. Moreover, we validated the correlation by confirming that the results from Beckman AU DxC had around 6% lower bias comparing with LC-MS/MS. Turnaround time serves as a critical quality indicator for evaluating testing process effectiveness and efficiency, as well as clinician and patient satisfaction. The implementation of in-house clozapine testing significantly improved pre-analytical, analytical, and post-analytical Turnaround times.
B-305 High-risk HPV Scenario Among Young People: Data From a Clinical Laboratory (2019-2023)
Authors: Feres M C , Perez B B , Souza M F , Ramadan-Boscolo D R , Tufik S 
Published: October 2024

Abstract

Background
Human papillomavirus (HPV) infection is the most common sexually transmitted infections and occurs early after the start of sexual life. There are more than 150 types of HPV, classified considering the affected area, symptoms, and oncogenic potential. The types of HPV that cause cancerous lesions are classified as high-risk HPV types. HPV is the main cause of cervical cancer in women and is strongly associated with penile cancer in men. Despite the existence of vaccination, it is still not easily accessible to the entire population of Brazil. In this context, the authors are periodically analyzing the positivity of high-risk HPV infection in secretion and cell scraping samples.

Methods
14,806 results were analyzed from a laboratory in São Paulo/Brazil. 4,935 real-time PCR tests were carried out from January/2019 to December/2023 for the detection of HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68 high risk types. In this study, there was a special focus on HPV types 16 and 18, as they are the main high-risk types for cervical cancer. The other high-risk genotypes were detected, but not differentiated.

Results
The most ages affected by the infection in both sexes were 25 to 40 years old. Infections with other high-risk types HPV were more frequent in relation to types 16 and 18, Table 1.

Conclusions
Although the male population represented only 1.19% of processes tests, a higher frequency of HPV positive results was detected (9.04%) compared to female patients (7.55%).
B-330 Reducing Inappropriate Fecal Immunochemical Test
Authors: Cai F , Gifford J L , Bourbonnie J , Sadrzadeh H 
Published: October 2024

Abstract

Background
Colorectal cancer is the third most common cancer worldwide. The risk of colorectal cancer increases with age and predominantly affects individuals over the age of 50. Regular screening is crucial for early detection and prevention of colorectal cancer. Pre-cancerous polyps and colorectal cancers can bleed into the gastrointestinal tract. While the presence of blood in the stool cannot always be seen visually, it can be detected by the Fecal Immunochemical Test (FIT), currently the most sensitive method for directly measuring hemoglobin in this specimen type. In our province, FIT is recommended for testing average-risk asymptomatic patients aged 50 to 74 every 1-2 years. Patients aged 40 to 49 or 75 to 84 can be tested if they meet specific criteria. Like many other tests in the lab, FIT can be used inappropriately. The focus of this study was to examine the utilization of FIT in our institution.

Methods
Data were collected from our institution's laboratory information system for the FIT performed on-site from July to December 2023.

Results
We performed 91,545 FIT tests during the 6-month period with an overall positive rate of 6.8%. Of the total tests performed, 87.9% were for patients aged 50-74 years, 10.6% for patients aged 40-49 or 75-84 years, and 1.2% for patients outside the approved age range. Each year, we performed over 2,000 FIT tests for patients outside the accepted screening age, with an estimated cost of over 30,000 CAD.

Conclusions
Our results showed a significant number of FITs were ordered inappropriately by healthcare providers. Considering the relatively high cost of FIT kits, labor, reagents, etc., the overall cost per reportable is significant. Thus, we have started engaging healthcare providers involved in FIT testing to strategize approaches to improve utilization.
The CsTIE1–CsAGL16 module regulates lateral branch outgrowth and drought tolerance in cucumber
Authors: Chen Jiacai , Chen Guangxin , Guo Jingyu , He Yuting , Liu Liu , Wang Shaoyun , Gu Chaoheng , Han Lijie , Li Min , Song Weiyuan , Wang Liming , Zhang Xiaolan , Zhao Jianyu 
Published: October 2024

Abstract
Drought stress and lateral branches are both important factors affecting crop yield. Cucumber is a widely planted vegetable crop that requires a large amount of water during its production and varieties with few lateral branches are preferred. However, the mechanisms regulating cucumber drought tolerance and lateral branch development remain largely unclear. The MADS-box transcription factor AGAMOUS-LIKE 16 (CsAGL16) was recently found to be a key positive regulator in cucumber shoot branching acting by stimulating abscisic acid (ABA) catabolism. In this study, we demonstrated that cucumber TCP interactor containing EAR motif protein 1 (CsTIE1) directly interacts with CsAGL16 at protein level and promotes lateral branch outgrowth through the CsAGL16–CsCYP707A4 mediated ABA pathway in cucumber. Additionally, mutation of CsAGL16 resulted in decreased drought tolerance, while overexpression of CsAGL16 significantly enhanced drought tolerance in cucumber. Similarly, the drought resistance of Cstie1 mutants was significantly reduced. However, overexpression of CsAGL16 can enhance the drought tolerance of Cstie1 mutants and promote their lateral branch outgrowth. These results indicated that the CsTIE1–CsAGL16 module was crucial for both lateral branch development and drought response, providing a strategy for cultivating drought-tolerant cucumber varieties with appropriate branch outgrowth.
Voters Share Polls That Say What They Want to Hear: Experimental Evidence From Spain and the USA
Authors: Fernández-Roldán Alejandro , Barnfield Matthew 
Published: October 2024

Abstract
Pre-election polls are published continuously, particularly in the run-up to elections. Increasingly, polls are commissioned by the media and gain traction through their propagation on social media. But polls differ along many dimensions, including in their estimated vote shares and the corresponding portrayal of the state of public opinion. We rely on recent evidence to argue that these factors are likely to affect people’s willingness to share polls with their networks. To test this claim, we conduct two studies. In the first, we expose Spanish voters to a random selection of recent, real, 2023 general election vote intention polls. In the second, a conjoint analysis presents US voters with abstract, hypothetical 2024 presidential election polls. Across both studies, we find no evidence of any effect of polling firms, fieldwork dates, or sample sizes on intentions to share polls. Above all, our results suggest that the main factor consistently affecting voters’ proclivity to share polls is the result of the poll itself. Our findings are consistent with the literature that suggests that voters’ reception of poll results is usually driven by directional goals, and may have significant implications in light of the unique epistemic value of reposting on social media.
Non-Density of the Exceptional Components of the Noether–Lefschetz Locus
Authors: Baldi Gregorio , Klingler Bruno , Ullmo Emmanuel 
Published: October 2024

Abstract
We study when the Picard group of smooth surfaces of degree $d\geq 5$ in $\mathbb{P}^{3}$ acquires extra classes. In particular we show that the so-called exceptional components of the Noether–Lefschetz locus are not Zariski dense. This answers a 1991 question of C. Voisin. We also obtain similar results for the Noether–Lefschetz locus for suitable $(Y,L)$, where $Y$ is a smooth projective three-fold and $L$ a very ample line bundle. Both results are applications of the Zilber–Pink viewpoint recently developed by the authors for arbitrary (polarized, integral) variations of Hodge structures.
Large-Angle Rocking Beam Electron Diffraction of Large Unit Cell Crystals Using Direct Electron Detector
Authors: Busch Robert , Ni Hsu-Chih , Shao Yu-Tsun , Zuo Jian-Min 
Published: October 2024

Abstract
We report a large-angle rocking beam electron diffraction (LARBED) technique for electron diffraction analysis. Diffraction patterns are recorded in a scanning transmission electron microscope (STEM) using a direct electron detector with large dynamical range and fast readout. We use a nanobeam for diffraction and perform the beam double rocking by synchronizing the detector with the STEM scan coils for the recording. Using this approach, large-angle convergent beam electron diffraction (LACBED) patterns of different reflections are obtained simultaneously. By using a nanobeam, instead of a focused beam, the LARBED technique can be applied to beam-sensitive crystals as well as crystals with large unit cells. This paper describes the implementation of LARBED and evaluates the performance using silicon and gadolinium gallium garnet crystals as test samples. We demonstrate that our method provides an effective and robust way for recording LARBED patterns and paves the way for quantitative electron diffraction of large unit cell and beam-sensitive crystals.
Utilization of Advanced Microscopy Techniques and Energy-dispersive X-ray Spectroscopy to Characterize Three Piper Species Related to Kava
Authors: Adams Sebastian John , Chittiboyina Amar G , Khan Ikhlas A 
Published: October 2024

Abstract
Macro- and microscopic techniques have long been used to describe plant materials and establish plant structural profiles. These techniques are commonly used in botanical authentication to identify the genuine and closely allied species used in botanical research. Advanced microscopic techniques were used in this study to differentiate three different Piper species used as kava or kava-kava. The genuine species is Piper methysticum and the other two species commonly called false-kava or kava-kava, are Piper auritum and Piper excelsum. Macroscopic characteristics, including a black-spotted stem and fibrous root, are characteristic of P. methysticum, whereas the stem of P. auritum is greenish with no spots, and the P. excelsum stem is purple-pink. Microscopic attributes include the characteristic collenchyma of stems and the pattern of arrangement of peripheral and medullary vascular bundles. The starch grains are smaller in P. excelsum than in the other two species. Energy-dispersive X-ray spectroscopy analysis of the crystals indicates the expected calcium, magnesium, and silica, along with lesser amounts of sodium, and potassium. The crystals present in the Piper species vary in shape, size, and elemental composition. Combining macro- and microscopical techniques and resulting characteristics are instrumental in differentiating the three Piper species.
Dietary protein intake and the tubular handling of indoxyl sulfate
Authors: Lauriola Mara , Farré Ricard , Dejongh Sander , de Loor Henriette , Evenepoel Pieter , Masereeuw Rosalinde , Zadora Ward , Meijers Björn 
Published: October 2024

ABSTRACT

Background
Chronic kidney disease (CKD) patients are advised to limit their protein intake. A high protein diet is known to induce glomerular hyperfiltration, as well as hypertrophy of the remnant kidney, and glomerulosclerosis. Whether the diet causes changes in kidney tubule transport via gut microbiome metabolites is still unknown. We hypothesized that protein intake affects not only the intestinal generation and absorption, but also the kidney disposal of microbial amino acid metabolites.

Methods
We combined data from animal models and human studies. 5/6th nephrectomy rats were administered a high (HP) or low-protein (LP) diet for 7 weeks. Plasma and urine concentration of the uremic toxins (UTs) indoxyl sulfate (IS), p-cresyl sulfate (PCS) and p-cresyl glucuronide (PCG) were measured. Their fractional excretion (FE) was calculated. The expression of kidney membrane transporters organic anion transporter 1 (OAT1), OAT3, BCRP, OCT2 and MRP4 was analyzed. Differences in FE of UTs between individuals with higher and lower protein intake in two CKD cohorts were sought.

Results
CKD rats on an HP diet showed increased plasma levels of PCS and PCG but not IS compared with rats on an LP diet. Conversely, urinary excretion and FE of IS were higher in the HP CKD group. BCRP, MRP4 and OCT2 were not influenced by the diet. OAT1 and OAT3 were upregulated in the HP CKD group. In two independent cohorts of CKD patients, individuals with a high dietary protein intake showed a significantly higher FE of IS.

Conclusions
A HP diet leads to a higher generation and/or absorption of amino acid–derived UT precursors in CKD rodent models and humans, most likely via gut microbiome modulation. We demonstrate that dietary protein intake modulates transcription and expression of OAT1 and OAT3, corroborating the existence of the remote sensing and signaling hypothesis. Dietary protein intake influences kidney physiology beyond glomerular filtration.