bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance Analysis of Liquid-to-Air Heat Exchanger of High-Power Density Racks
Authors: Heydari Ali , Gharaibeh Ahmad R. , Tradat Mohammad , Soud Qusai , Manaserh Yaman , Radmard Vahideh , Eslami Bahareh , Rodriguez Jeremy , Sammakia Bahgat 
Published: May 2024

Abstract
The ability of traditional room-conditioning systems to accommodate expanding information technology loads is limited in contemporary data centers (DCs), where the storage, storing, and processing of data have grown quickly as a result of evolving technological trends and rising demand for online services, which has led to an increase in the amount of waste heat generated by IT equipment. Through the implementation of hybrid air and liquid cooling technologies, targeted, on-demand cooling is made possible by employing a variety of techniques, which include but are not limited to in-row, overhead, and rear door heat exchanger (HX) cooling systems. One of the most common liquid cooling techniques will be examined in this study based on different conditions for high-power density racks (+50 kW). This paper investigates the cooling performance of a liquid-to-air in-row coolant distribution unit (CDU) in test racks containing seven thermal test vehicles (TTVs) under various conditions, focusing on cooling capacity and HX effectiveness under different supply air temperatures (SAT). This test rig has the necessary instruments to monitor and analyze the experiments on both the liquid coolant and the air sides. Moreover, another experiment is conducted to assess the performance of the CDU that runs under different control fan schemes, as well as how the change of the control type will affect the supply fluid temperature and the TTV case temperatures at 10%, 50%, and 100% of the total power. Finally, suggestions for the best control fan scheme to use for these systems and units are provided at the conclusion of the study.
Comparison of the performance of two targeted metagenomic virus capture probe-based methods using reference control materials and clinical samples
Authors: Mourik Kees , Sidorov Igor , Carbo Ellen C. , van der Meer David , Boot Arnoud , Kroes Aloysius C. M. , Claas Eric C. J. , Boers Stefan A. , de Vries Jutte J. C. 
Published: May 2024

ABSTRACT

Viral enrichment by probe hybridization has been reported to significantly increase the sensitivity of viral metagenomics. This study compares the analytical performance of two targeted metagenomic virus capture probe-based methods: (i) SeqCap EZ HyperCap by Roche (ViroCap) and (ii) Twist Comprehensive Viral Research Panel workflow, for diagnostic use. Sensitivity, specificity, and limit of detection were analyzed using 25 synthetic viral sequences spiked in increasing proportions of human background DNA, eight clinical samples, and American Type Culture Collection (ATCC) Virome Virus Mix. Sensitivity and specificity were 95% and higher for both methods using the synthetic and reference controls as gold standard. Combining thresholds for viral sequence read counts and genome coverage [respectively 500 reads per million (RPM) and 10% coverage] resulted in optimal prediction of true positive results. Limits of detection were approximately 50–500 copies/mL for both methods as determined by ddPCR. Increasing proportions of spike-in cell-free human background sequences up to 99.999% (50 ng/mL) did not negatively affect viral detection, suggesting effective capture of viral sequences. These data show analytical performances in ranges applicable to clinical samples, for both probe hybridization metagenomic approaches. This study supports further steps toward more widespread use of viral metagenomics for pathogen detection, in clinical and surveillance settings using low biomass samples.

IMPORTANCE
Viral metagenomics has been gradually applied for broad-spectrum pathogen detection of infectious diseases, surveillance of emerging diseases, and pathogen discovery. Viral enrichment by probe hybridization methods has been reported to significantly increase the sensitivity of viral metagenomics. During the past years, a specific hybridization panel distributed by Roche has been adopted in a broad range of different clinical and zoonotic settings. Recently, Twist Bioscience has released a new hybridization panel targeting human and animal viruses. This is the first report comparing the performance of viral metagenomic hybridization panels.
Temperate phage-antibiotic synergy across antibiotic classes reveals new mechanism for preventing lysogeny
Authors: Al-Anany Amany M. , Fatima Rabia , Nair Gayatri , Mayol Jordan T. , Hynes Alexander P. 
Published: May 2024

ABSTRACT

A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged
Escherichia coli
with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some β-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.

IMPORTANCE
The lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to “wake” the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.
Post-market surveillance of six COVID-19 point-of-care tests using pre-Omicron and Omicron SARS-CoV-2 variants
Authors: Exner Hannah M. , Gregorchuk Branden S. J. , Castor AC-Green , Crisostomo Leandro , Kolsun Kurt , Giesbrecht Shayna , Dust Kerry , Alexander David C. , Bolaji Ayooluwa , Quill Zoe , Head Breanne M. , Meyers Adrienne F. A. , Sandstrom Paul , Becker Michael G. 
Published: May 2024

ABSTRACT

Post-market surveillance of test performance is a critical function of public health agencies and clinical researchers that ensures tests maintaining diagnostic characteristics following their regulatory approval. Changes in product quality, manufacturing processes over time, or the evolution of new variants may impact product performance. During the COVID-19 pandemic, a plethora of point-of-care tests (POCTs) was released onto the Canadian market. This study evaluated the performance characteristics of several of the most widely distributed POCTs in Canada, including four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT). All tests were challenged with 149 SARS-CoV-2 clinical positives, including multiple variants up to and including Omicron XBB.1.5, as well as 29 clinical negatives. Results were stratified based on whether the isolate was Omicron or pre-Omicron as well as by reverse transcriptase quantitative PCR Ct value. The test performance of each POCT was consistent with the manufacturers' claims and showed no significant decline in clinical performance against any of the variants tested. These findings provide continued confidence in the results of these POCTs as they continue to be used to support decentralized COVID-19 testing. This work demonstrates the essential role of post-market surveillance in ensuring reliability in diagnostic tools.

IMPORTANCE
Post-market surveillance of diagnostic test performance is critical to ensure their reliability after regulatory approval. This is especially critical in the context of the COVID-19 pandemic as the use of point-of-care tests (POCTs) became widespread. Our study focused on four rapid antigen tests (Abbott Panbio, BTNX Rapid Response, SD Biosensor, and Quidel QuickVue) and two molecular tests (Abbott ID NOW and Lucira Check IT) that were widely distributed across Canada, assessing their performance using many SARS-CoV-2 variants, including up to Omicron subvariant XBB.1.5. Overall, we found no significant difference in performance against any variant, reinforcing confidence in their use. As concerns in test efficacy have been raised by news outlets, particularly regarding the BTNX Rapid Response, this work is even more timely and crucial. Our research offers insights into the performance of widely used COVID-19 POCTs but also highlights the necessity for post-market surveillance.
Multi-scale, open-system magmatic and sub-solidus processes contribute to the chemical and isotopic characteristics of the Jurassic Guadalupe Igneous Complex, Sierra Nevada, California, USA
Authors: Ratschbacher Barbara C. , Ardill Katie , Keller C. Brenhin , Schoene Blair , Paterson Scott R. , Putirka Keith D. , Lackey Jade Star , Paige Matthew L. 
Published: May 2024

Abstract
The chemical and isotopic characteristics of a solidified pluton represent the integration of magmatic and sub-solidus processes operating across a range of spatial and temporal scales during pluton construction, crystallization, and cooling. Disentangling these processes and understanding where chemical and isotopic signatures were acquired requires the combination of multiple tools tracing processes at different time and length scales. We combine whole-rock oxygen and Sr-Nd isotopes, zircon oxygen isotopes and trace elements, and mineral compositions with published high-precision U-Pb zircon geochronology to evaluate differentiation within the bimodal Guadalupe Igneous Complex, Sierra Nevada, California (USA). The complex was constructed in ~300 k.y. between 149 and 150 Ma. Felsic magmas crystallized as centimeter- to meter-sized segregations in gabbros in the lower part of the complex and as granites and granophyres structurally above the gabbros. A central mingling zone separates the mafic and felsic units. Pluton-wide δ18O(whole-rock), δ18O(zircon), and Sr-Nd isotopic ranges are too large to be explained by in situ, closed-system differentiation, instead requiring open-system behavior at all scales. Low δ18O(whole-rock) and δ18O(zircon) values indicate assimilation of hydrothermally altered marine host rocks during ascent and/or emplacement. In situ differentiation processes operated on a smaller scale (meters to tens of meters) for at least ~200 k.y. via (1) percolation and segregation of chemically and isotopically diverse silicic interstitial melt from a heterogeneous gabbro mush; (2) crystal accumulation; and (3) sub-solidus, high-temperature, hydrothermal alteration at the shallow roof of the complex to modify the chemical and isotopic characteristics. Whole-rock and mineral chemistry in combination with geochronology allows deciphering open-system differentiation processes at the outcrop to pluton scale from magmatic to sub-solidus temperatures over time scales of hundreds of thousands to millions of years.
A randomized phase II trial to examine modified vaccinia Ankara-5T4 vaccine in patients with relapsed asymptomatic ovarian cancer (TRIOC)
Authors: Michael Agnieszka , Wilson William , Sunshine Sunny , Annels Nicola , Harrop Richard , Blount Daniel , Pandha Hardev , Lord Rosemary , Ngai Yen , Nicum Shibani , Stylianou Laura , Gwyther Stephen , McNeish Iain A , Hackshaw Allan , Ledermann Jonathan 
Published: May 2024

Background
Immunotherapy directed at 5T4 tumor antigen may delay the need for further chemotherapy. An attenuated modified vaccinia Ankara virus containing the gene encoding for 5T4 (MVA-5T4) was studied in asymptomatic relapsed ovarian cancer.

Objective
To assess the effectiveness and safety of MVA-5T4 as treatment for asymptomatic relapsed ovarian cancer.

Methods
TRIOC was a phase II randomized (1:1), placebo-controlled, double-blind multicenter study. The primary aim was to assess the effectiveness and safety of MVA-5T4 as a treatment for asymptomatic patients with relapsed ovarian cancer. Eligible patients had International Federation of Gynecology and Obstetrics (FIGO) stage IC1–III or IVA epithelial ovarian, fallopian tube, or primary peritoneal carcinoma, Eastern Cooperative Oncology Group (ECOG) 0–1, with relapse defined by a rise in CA-125 to twice the upper limit of normal or low-volume disease on CT scan. The primary endpoint was disease progression (including deaths from ovarian cancer) at 25 weeks. Following a brief suspension, the trial restarted as a single-arm study. The revised single-arm design required 45 evaluable patients treated with MVA-5T4 to detect a 25-week progression rate of 50%, assuming an expected 70% rate without MVA-5T4; 85% power with one-sided 5% significance.

Results
A total of 94 eligible patients were recruited, median age was 65 years (range 42–82), median follow-up 34 months (range 2–46). Overall, 59 patients received MVA-5T4 and 35 patients received placebo. The median number of MVA-5T4 injections received was 7 (range 0–9), compared with a median of 6 (range 1–12) for patients receiving placebo. Median progression-free survival was the same in both arms (3.0 months). The 25-week progression rate was similar in both arms: 80.0% for patients treated with MVA-5T4 and 85.7% for those receiving placebo (risk difference −5.7%, 95% CI −21.4% to 10.0%). Median time to clinical intervention was improved with MVA-5T4: 7.6 months (range 6.7–9.5) vs 5.6 (range 4.9–7.6),

Conclusion
MVA-5T4 vaccination in patients with asymptomatic relapse was well-tolerated but did not improve the progression rate at 25 weeks. The majority of patients who received MVA-5T4 had clinical intervention later than those assigned to placebo.

Trial registration number

NCT01556841
.
Data discrepancies: Italian ministry reports on abortion, contextualised
Authors: Pullan Danielle , Gannon Payton 
Published: May 2024

The Italian Ministry of Health reports annually on activities related to abortion and fertility, providing quantitative data that looks ripe for analysis. Actors ranging from activists to medical providers to European courts have criticised the data as misleading, but the Ministry reports have not changed. In this piece, we bring together different perspectives on this data from inside and outside academia and offer guidance on how it should—and should not—be used in research.
In this article, we collect a wide variety of publications ranging from civil society groups’ reports to court decisions, academic articles and investigative reporting and harmonise the way they engage with the Italian Ministry of Health’s data regarding abortion and particularly conscientious objection.
Analyses rooted in the demographic and medical data about abortion seekers, the abortion rates over time, the different methods of abortion, etc are trustworthy and can be used to extrapolate levels of abortion access. This dataset on conscientious objectors systematically undercounts objectors, implying a false equivalence between people who do not object and people who actually work in an abortion service. We recommend that the Ministry report both the number of objectors and the number of medical doctors working in abortion services.
The Italian Ministry of Health produces some valuable data about abortion, but conscientious objection is the key feature of abortion access in Italy, and this key datapoint is flawed. The Ministry could improve clarity and increase citizens’ trust in government reports by adding data on the number of abortion providers.
Intraspecific variation in the functional response of an invasive crayfish under different temperatures
Authors: Chicatun Victoria , Sheppard Noemie L. M. , Ricciardi Anthony 
Published: May 2024

Non-native species can react to changes to their thermal environment by altering their feeding behaviour, thereby potentially causing shifts in predator–prey dynamics and competitive dominance over native species. In this study, we measured intraspecific variation in the functional response (i.e., predation rate as a function of prey density) of the rusty crayfish Faxonius rusticus (Girard, 1852) at two temperatures (18 °C and 26 °C) in the laboratory. We compared six invasive populations spanning a 2° latitudinal gradient in eastern North America to test the prediction that under warmer conditions individuals from more southerly populations exhibit a higher functional response than those from northern populations. Temperature, latitude, and the interaction between these two variables had significant effects on attack rates and handling times of individual crayfish from the tested populations. Contrary to our prediction, the attack rates of individuals from northern populations were consistently higher than those from southern populations at both temperatures. We propose that these interpopulation differences in functional response could arise, at least in part, from countergradient selection. Our results suggest that climate warming promotes spatiotemporal variation in per capita effects across latitudinally distributed populations of aquatic invasive species.
Abstract A001: Urine-based liquid biopsy test for the detection of residual bladder cancer in radical cystectomy patients
Authors: Abbosh Philip H. , Valentine Henkel , Arya Rhea 
Published: May 2024

Abstract
One commonly employed management strategy for muscle-invasive bladder cancer (MIBC) is neoadjuvant chemotherapy followed by radical cystectomy (RC) and urinary diversion. Approximately 35% of patients achieve a pathologic complete response (pCR) when evaluated from RC specimens. RC with urinary diversion is a life-altering operation with high complication rates and therefore determining who are complete responders would improve quality of life and could decrease costs and still achieve a high cure rate via RC avoidance. Unfortunately, current methods cannot accurately identify complete responders. Our lab has developed a urine-based liquid biopsy test in which DNA isolated from urine and germline is isolated and subjected to panel exome sequencing for enumeration of somatic variants. This occurs under the premise that tumor DNA identified (as mutant alleles) is a marker of residual disease while the absence of tumor DNA (meaning the absence of mutant alleles) can indicate a pCR. A 60 gene panel was designed to be used for exonic sequencing of urinary DNA (uDNA) to identify mutations indicative of bladder cancer or therapeutic targets. We have shown that most mutations in tumor tissue (Mt) are detectable as mutations in urine (Mu). We also showed that the presence or absence of residual Mu after completion of chemotherapy strongly associates with residual disease or pCR at the time of RC, respectively. Therefore, this test could be used after neoadjuvant therapy to better identify patients for RC avoidance. We optimized this test by studying pre-analytical factors affecting the yield, purity, and integrity of uDNA and the quality of sequencing data using prospectively collected samples from patients with MIBC. We are also in the process of testing commercial and novel preservatives to optimize DNA integrity, yield, and mutation detection accuracy to enable temporary ambient temperature storage without compromising mutation detection, permitting shipping/centralized testing. Lastly, we are comparing two library preparation approaches. Study of these preanalytical factors has increased the number of Mu that can be detected and were applied to a cohort of patients who underwent bladder sparing curative-intent treatment in a prospective clinical trial. Studies described herein will enable liquid biopsy tests to accurately identify patients with pCR after neoadjuvant therapy and might safely avoid radical cystectomy.
Citation Format: Philip H. Abbosh, Henkel Valentine, Rhea Arya. Urine-based liquid biopsy test for the detection of residual bladder cancer in radical cystectomy patients [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr A001.