PRECISION.array: An R Package for Benchmarking microRNA Array Data Normalization in the Context of Sample Classification

We present a new R package PRECISION.array for assessing the performance of data normalization methods in connection with methods for sample classification. It includes two microRNA microarray datasets for the same set of tumor samples: a re-sampling-based algorithm for simulating additional paired datasets under various designs of sample-to-array assignment and levels of signal-to-noise ratios and a collection of numerical and graphical tools for method performance assessment. The package allows users to specify their own methods for normalization and classification, in addition to implementing three methods for training data normalization, seven methods for test data normalization, seven methods for classifier training, and two methods for classifier validation. It enables an objective and systemic evaluation of the operating characteristics of normalization and classification methods in microRNA microarrays. To our knowledge, this is the first such tool available. The R package can be downloaded freely at https://github.com/LXQin/PRECISION.array

Risk Factors for Mortality Among Critical Acute Pancreatitis Patients with Carbapenem-Resistant Organism Infections and Drug Resistance of Causative Pathogens

IntroductionCarbapenem-resistant organisms (CRO) have emerged as a major global public health threat, but their role in critical acute pancreatitis (CAP) is still not defined. Our study aims to investigate risk factors associated with mortality and drug resistance among CAP patients with CRO infection.MethodsThe clinical characteristics of CAP patients with CRO infection and drug resistance of causative pathogens from January 1, 2016, to October 1, 2021, were reviewed retrospectively. Independent risk factors for mortality were determined via univariate and multivariate analyses.ResultEighty-two CAP patients suffered from CRO infection, with mortality of 60.0%. The independent risk factors for mortality were procalcitonin > 5 ng/L (hazard ratio = 2.300, 95% confidence interval = 1.180-4.484, P = 0.014) and lactic acid > 2 mmol/L (hazard ratio = 2.101, 95% confidence interval = 1.151-3.836, P = 0.016). The pancreas was the main site of infection, followed by lung, bloodstream and urinary tract. Klebsiella pneumoniae and Acinetobacter baumannii were the main pathogenic bacteria of CRO strains with extensive antibiotic resistance (> 60%) to 6 of 8 common antibiotics, except sulfamethoxazole (56.3%) and tigecycline (33.2%).ConclusionCRO infection has become a serious threat for CAP patients, with high rates of mortality. Procalcitonin and lactic acid represent two independent risk factors for mortality in CAP patients with CRO infection. Klebsiella pneumoniae and Acinetobacter baumannii are the primary categories of CRO pathogens. Greater efforts are needed for early prevention and prompt treatment of CRO infections in CAP patients

The safety of colorectal cancer surgery during the COVID-19: a systematic review and meta-analysis

BackgroundThe ongoing coronavirus disease 2019 (COVID-19) pandemic has placed unprecedented pressure on the healthcare systems. This study evaluated the safety of colorectal cancer (CRC) surgery during the COVID-19 pandemic.MethodsA systematic review and meta-analysis were performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (PROSPERO ID: CRD 42022327968). Relevant articles were systematically searched in the PubMed, Embase, Web of Science, and Cochrane databases. The postoperative complications, anastomotic leakage, postoperative mortality, 30-day readmission, tumor stage, total hospitalization, postoperative hospitalization, preoperative waiting, operation time, and hospitalization in the intensive care unit (ICU) were compared between the pre-pandemic and during the COVID-19 pandemic periods.ResultsAmong the identified 561 articles, 12 met the inclusion criteria. The data indicated that preoperative waiting time related to CRC surgery was higher during the COVID-19 pandemic (MD, 0.99; 95%CI, 0.71–1.28; p < 0.00001). A similar trend was observed for the total operative time (MD, 25.07; 95%CI, 11.14–39.00; p =0.0004), and on T4 tumor stage during the pandemic (OR, 1.77; 95%CI, 1.22–2.59; p=0.003). However, there was no difference in the postoperative complications, postoperative 90-day mortality, anastomotic leakage, and 30-day readmission times between pre-COVID-19 pandemic and during the COVID-19 pandemic periods. Furthermore, there was no difference in the total hospitalization time, postoperative hospitalization time, and hospitalization time in ICU related to CRC surgery before and during the COVID-19 pandemic.ConclusionThe COVID-19 pandemic did not affect the safety of CRC surgery. The operation of CRC during the COVID-19 pandemic did not increase postoperative complications, postoperative 90-day mortality, anastomotic leakage, 30-day readmission, the total hospitalization time, postoperative hospitalization time, and postoperative ICU hospitalization time. However, the operation of CRC during COVID-19 pandemic increased T4 of tumor stage during the COVID-19 pandemic. Additionally, the preoperative waiting and operation times were longer during the COVID-19 pandemic. This provides a reference for making CRC surgical strategy in the future.Systematic review registrationhttps://www.crd.york.ac.uk/prospero/, identifier CRD42022327968

The Perturbation of Infant Gut Microbiota Caused by Cesarean Delivery Is Partially Restored by Exclusive Breastfeeding

Early establishment of the infant gut microbiome has been attributed to various environmental factors that may influence long-term health. The aim of this study was to determine the single and combined impacts of the delivery mode, feeding pattern and postnatal antibiotic exposure on the initial establishment of infant gut microbiome at 6 weeks postpartum. A cross-sectional study was conducted at a single center in China. Fecal samples were collected from 120 infants at 6 weeks postpartum. The V3-V4 regions of 16S rRNA gene were analyzed by Illumina sequencing, and clinical information was obtained from medical records and questionnaire survey. Compared with vaginally delivered infants, the gut microbial community structure of cesarean delivered infants were significantly different (P = 0.044), in parallel with the decreased relative abundance of Bifidobacterium (P = 0.028), which contrasts with the normal gut microbial establishment. Using the vaginally delivered and exclusively breastfed (VB) infants as a reference, the comparative analysis of cesarean delivered and exclusively breastfed (CB) infants with cesarean delivered and mixed-fed (CM) infants showed that both within- and between-group UniFrac distance were significantly smaller in CB infants (P < 0.001, P < 0.001). LEfSe analysis showed that the relative abundances of Enterococcus, Veillonella, and Faecalibacterium were significantly different between CB and CM infants, whereas the relative abundances of those genera in VB infants were close to those of CB infants, and distinct from those of CM infants. Additionally, no significant difference of microbial composition, alpha diversity, or community structure was observed between postnatal antibiotics exposed infants and unexposed infants. In summary, delivery mode had a significant impact on the infant gut microbial community structure and composition, and the gut microbiota was disturbed in infants delivered by cesarean section. However, our study showed that this disturbance of gut microbiota in cesarean delivered infants was partially restored by exclusive breastfeeding in comparison with mixed feeding. No distinct impact of postnatal antibiotic exposure on infant gut microbiome was found at 6 weeks of age

A Tunable Transition Metal Dichalcogenide Entangled Photon-Pair Source

Entangled photon-pair sources are at the core of quantum applications like quantum key distribution, sensing, and imaging. Operation in space-limited and adverse environments such as in satellite-based and mobile communication requires robust entanglement sources with minimal size and weight requirements. Here, we meet this challenge by realizing a cubic micrometer scale entangled photon-pair source in a 3R-stacked transition metal dichalcogenide crystal. Its crystal symmetry enables the generation of polarization-entangled Bell states without additional components and provides tunability by simple control of the pump polarization. Remarkably, generation rate and state tuning are decoupled, leading to equal generation efficiency and no loss of entanglement. Combining transition metal dichalcogenides with monolithic cavities and integrated photonic circuitry or using quasi-phasematching opens the gate towards ultrasmall and scalable quantum devices

Proposed clinical phases for the improvement of personalized treatment of checkpoint inhibitor–related pneumonitis

BackgroundCheckpoint inhibitor–related pneumonitis (CIP) is a lethal immune-related adverse event. However, the development process of CIP, which may provide insight into more effective management, has not been extensively examined.MethodsWe conducted a multicenter retrospective analysis of 56 patients who developed CIP. Clinical characteristics, radiological features, histologic features, and laboratory tests were analyzed. After a comprehensive analysis, we proposed acute, subacute, and chronic phases of CIP and summarized each phase’s characteristics.ResultsThere were 51 patients in the acute phase, 22 in the subacute phase, and 11 in the chronic phase. The median interval time from the beginning of CIP to the different phases was calculated (acute phase: ≤4.9 weeks; subacute phase: 4.9~13.1 weeks; and chronic phase: ≥13.1 weeks). The symptoms relieved from the acute phase to the chronic phase, and the CIP grade and Performance Status score decreased (P<0.05). The main change in radiologic features was the absorption of the lesions, and 3 (3/11) patients in the chronic phase had persistent traction bronchiectasis. For histologic features, most patients had acute fibrinous pneumonitis in the acute phase (5/8), and most had organizing pneumonia in the subacute phase (5/6). Other histologic changes advanced over time, with the lesions entering a state of fibrosis. Moreover, the levels of interleukin-6, interleukin-10 and high-sensitivity C-reactive protein (hsCRP) increased in the acute phase and decreased as CIP progressed (IL-6: 17.9 vs. 9.8 vs. 5.7, P=0.018; IL-10: 4.6 vs 3.0 vs. 2.0, P=0.041; hsCRP: 88.2 vs. 19.4 vs. 14.4, P=0.005).ConclusionsThe general development process of CIP can be divided into acute, subacute, and chronic phases, upon which a better management strategy might be based devised

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

High Efficiency Uranium(VI) Removal from Wastewater by Strong Alkaline Ion Exchange Fiber: Effect and Characteristic

In this study, we analyzed the removal efficiency of uranium(U(VI)) in wastewater at relatively low concentrations using strong alkaline ion exchange fiber (SAIEF). Static tests showed that the strong alkali fibers can purify U(VI) containing wastewater in a concentration range of 20–100 mg L−1 with an optimal pH of 10.5 and contact time of 15–30 min. Adsorption and desorption cycling tests indicated that, adsorbed uranium is easily desorbed by 0.1 mol L−1 HCl, and the fiber still maintained the original adsorption efficiency after eight cycles. According to dynamic penetration test results, the SAIEF saturation adsorption capacity was 423.9 mg g−1, and the effluent concentration of uranium through two series columns was less than 0.05 mg L−1, reaching the national standard for non-receiving water (GB23727-2009) SEM-EDS and FTIR analysis revealed that the functional group of SAIEF is CH2N+(CH3)3Cl−. Addotionally, the major forms of fiber exchange adsorption are (UO2)2CO3(OH)3−, UO2(CO)34− and UO2(OH)3−. The results indicate that the SAIEF is an excellent material for uranium removal