Individual Reading Research Articles

Accurate gene consensus at low nanopore coverage.

Nanopore technologies allow high-throughput sequencing of long strands of DNA at the cost of a relatively large error rate. This limits its use in the reading of amplicon libraries in which there are only a few mutations per variant and therefore they are easily confused with the sequencing noise. Consensus calling strategies reduce the error but sacrifice part of the throughput on reading typically 30 to 100 times each member of the library. In this work, we introduce SINGLe (SNPs In Nanopore reads of Gene Libraries), an error correction method to reduce the noise in nanopore reads of amplicons containing point variations. SINGLe exploits that in an amplicon library, all reads are very similar to a wild-type sequence from which it is possible to experimentally characterize the position-specific systematic sequencing error pattern. Then, it uses this information to reweight the confidence given to nucleotides that do not match the wild-type in individual variant reads and incorporates it on the consensus calculation. We tested SINGLe in a mutagenic library of the KlenTaq polymerase gene, where the true mutation rate was below the sequencing noise. We observed that contrary to other methods, SINGLe compensates for the systematic errors made by the basecallers. Consequently, SINGLe converges to the true sequence using as little as 5 reads per variant, fewer than the other available methods.

Impact of Nail Polish Colour on the Accuracy of Pulse Oximeter Reading in Healthy Individuals

Objective: To assess the effect of single-layered common nail polish colour on change in pulse oximeter reading.
 Study Design: Cross-sectional analytical study.
 Place and Duration of the Study: Combined Military Hospital, Peshawar, Pakistan, from Sep 2021 to Apr 2022.
 Methodology: Four hundred healthy females were included in the study that was normothermic, had an Oxygen saturation (SpO2) reading of 95% or more and do not have associated comorbidities, nailbed abnormalities or any history of trauma to limb. Individuals having any previous factors were excluded from the study. After informed consent, SpO2 was recorded using a portable infrared pulse oximeter in all four fingernails of the subjects at room temperature and then rechecked after the single-layered common nail polish was applied and dried. Red, green, black and purple were assigned to the index finger,middle finger, ring finger and little finger, respectively. In addition to oxygen saturation, other parameters, including age,gender, educational status, residence etc., were also recorded.
 Results: There was a statistically significant difference in oxygen saturation readings via portable infrared pulse oximeter in all four fingernails after applying single-layered common nail polish colours (p-value<0.0001). However, there was no clinically significant difference in oxygen saturation reading recorded in any individual.
 Conclusion: A single layer of common nail polish affected the SpO2 reading measured through a portable pulse oximeter. This should be kept in mind when evaluating such patients in emergency reception.

Evaluation of Inappropriate Positioning of Dosimeters in Medical Workers Based on Dose Equivalent Hp(10).

This report presents a new method to characterize the inappropriate positioning of dosimeters based on the dose equivalent Hp(10). The Hp(10) values of medical workers were measured monthly for 12 mo using two personal dosimeters. Using the ratio between the values of Hp(10) recorded from dosimeters worn over and under protective aprons [Hp(10) over and Hp(10) under , respectively], 670 pairs of dosimeter readings were categorized into a proper use group [Hp(10) over /Hp(10) under ≥ 5] and a misuse group [Hp(10) over /Hp(10) under < 5]. Following personal interviews, the readings in the misuse group were classified into the following six subgroups: "reversed," "sometimes reversed," "both under," "both over," "without apron," and "not specified." Ultimately, the scatter plot of "Hp(10) over - Hp(10) under " vs. Hp(10) over was identified as the most promising tool for clarifying the misuse patterns of dosimeters, as individual readings were mapped to the locations of the corresponding subgroups in the obtained graphs. Our results are expected to facilitate efficient and accurate usage of dosimeters by medical workers.

LBODP059 In-patient Hyperglycemia Among Non-critically Ill Patients Admitted At The University Of Santo Tomas Hospital, A Tertiary Teaching Hospital: A Prospective Study

Abstract Several societies provide in-hospital diabetes care guidelines on admission HbA1c, insulin initiation, sliding scale avoidance, and adoption of hypoglycemia protocol. This study aimed to determine the contemporary state of diabetes management and compliance to guidelines in the University of Santo Tomas Hospital, a tertiary teaching hospital, among non-critically ill patients from September-December 2021. A descriptive prospective study of in-patients with hyperglycemia was done. Exclusion criteria included hyperglycemic crisis, intensive care admission and gestational diabetes. Primary outcome was median capillary blood glucose (CBG) on admission compared to discharge and upon treatment modification stratified according to regimen and diagnoses (infection, surgery, diagnostic procedures and non-infectious medical). A total of 127 eligible patients were included with a mean age of 64 years with male predominance. Baseline median HbA1c was 7% [6.2-8.2]. The incidence of in-patient hyperglycemia (i. e., individual CBG reading &amp;gt;180 mg/dL) was 36% with highest proportion in the infection group. Fifty seven percent had at least one reading of hyperglycemia during hospital stay. The most common admission transition practice was resumption of home diabetes regimen with modified dose. The most common in-patient regimen was insulin therapy (largely, correctional scale alone, 47%) followed by oral hypoglycemic agents (OHA), mostly dipeptidyl peptidase inhibitors. Change in CBG among the basal-bolus group was significantly higher compared to OHA (p 0. 0002), insulin+OHA (p 0. 0183), basal (p 0. 0187), and correctional (p&amp;lt;0. 00001). Patients on insulin+OHA showed a significant change in percentage hyperglycemia across CBG readings (p 0. 0006). In the infection group, greatest median change in CBG was in basal-bolus (77mg/dL) followed by insulin+OHA (46mg/dL). Median change did not significantly differ by type of regimen with other diagnoses. Correctional scale was ordered in 95% of patients and was not associated with hypoglycemia (p 1. 000). There was no difference in the development of hypoglycemia by any type of regimen as well (p 0.134). Only elevated admission HbA1c was associated with persistent hyperglycemia (p 0. 050). Response to hyperglycemia differed (p&amp;lt;0. 0001) between endocrinologists (dose up-titration and shift to basal+bolus+OHA) and other services (dose maintenance). Percentage CBG on target did not differ between the two but compliance to discharge guidelines (provision of discharge, follow-up and dietary instructions) were lower among patients not referred to endocrinology (p &amp;lt;0. 0001). Basal-bolus still provide the most effective coverage followed by insulin+OHA even on infection group. For a more wholistic in-patient care, review of guidelines for non-endocrinology services is recommended to improve discharge transition practices. Presentation: No date and time listed

LBODP061 A Pilot Trial Of Continuous Glucose Monitoring Technology In The Perioperative Period

Abstract Objective To evaluate use of continuous glucose monitoring (CGM) technology in the perioperative setting by comparing CGM with concurrent point of care fingerstick blood glucose (BG) or arterial BG values, as indicated, in patients with hyperglycemia and/or diabetes mellitus undergoing surgery. To assess if grounding device correlated with loss of CGM signal as a prior study of CGM in the perioperative period noted intermittent signal loss during operative time. Methods A prospective cohort analysis of 94 participants with hyperglycemia and/or diabetes mellitus undergoing surgery of 3 hours duration was conducted using Dexcom G6 and/or Freestyle Libre 2. 0 CGM. CGMs were placed preoperatively and compared to standard of care BG checks in the perioperative setting. Correction insulin was administered based on fingerstick glucoses. Of those consented, 18 were excluded resulting in 76 enrolled subjects. Results Preliminary data for use of CGM in perioperative period analyzed 50 participants with Freestyle Libre 2. 0 CGM, 20 participants with Dexcom G6 CGM, and 6 participants with both devices worn simultaneously. Lost sensor data occurred for 3 participants wearing Dexcom G6 CGM and 10 participants wearing Freestyle Libre 2. 0 CGM, which affected 2 of the participants wearing both devices simultaneously. The absolute difference of Dexcom G6 CGM glucose readings compared to BG readings was 29.17 mg/dL (SD = 22.15). The absolute difference of Freestyle Libre 2. 0 CGM glucose readings compared to BG readings was 26.94 mg/dL (SD = 24.16). There was not a significant difference in averages of absolute change in glucose when comparing Dexcom G6 CGM to Freestyle Libre 2. 0 CGM when utilized simultaneously. Grounding devices utilized Megadyne grounding pad for use of bipolar cautery, monopolar cautery, and surgeries with da Vinci robot. Of the 13 participants with lost data, 3 patients had bipolar cautery reported as being used at least once and 10 participants with lost data utilized monopolar cautery. None of the 6 participants with surgery utilizing da Vinci robot had loss of CGM data. Conclusion Both Dexcom G6 and Freestyle Libre 2. 0 CGMs were able to be utilized in the perioperative setting and generally functioned well. Use of CGM provided more glycemic data and better characterized glycemic trends than individual BG readings. It is anticipated that this technology could improve prevention of hypoglycemic events and better glycemic control in the perioperative setting. Use of CGMs in the perioperative setting is a novel area of application that warrants further evaluation of this technology. Presentation: No date and time listed

Introduction: Form and Medium

Introduction: Form and Medium

A Review of Cell Operation Algorithm for 3D NAND Flash Memory

The size of the memory market is expected to continue to expand due to the digital transformation triggered by the fourth industrial revolution. Among various types of memory, NAND flash memory has established itself as a major data storage medium based on excellent cell characteristics and manufacturability; as such, the demand for increasing the bit density and the performance has been rapidly increasing. In this paper, we will review the device operation algorithm and techniques to improve the cell characteristics and reliability in terms of optimization of individual program, read and erase operation, and system level performance.

Genomic basis for early-life mortality in sharpsnout seabream

Mortality at early life stages of fishes is common in nature and can be shaped by stochastic and selective processes. Selective mortality has rarely been assessed in natural conditions but can now be studied by combining genomic data with information on different life stages that realates to fitness. Here we investigate selective mortality between settlers and six-month survivors of the sharpsnout seabream by genotype-phenotype/environmental association studies in three localities along a geographic gradient. We gathered information on 105 individuals at 85,031 SNPs, obtained from individual based 2b-RAD libraries, as well as 9 phenotypic and environmental variables derived from individual otolith readings. We found common signals across localities for potential selection, such as lower survival rates for individuals hatching earlier, growing faster and experiencing higher temperatures during their planktonic phase. We identified 122 loci with parallel significant association to phenotypic and environmental variables. Importantly, one of these loci mapped to the exonic region of the il20rb, a gene involved in immune response, in the phylogenetically closest reference genome, showing parallel frequency changes in non-synonymous mutations in the three studied populations. Further temporal assessments are needed to understand how polymorphisms that are key to selective mortality are maintained.

How Much Should You Care About Algorithmic Transparency as Manipulation?

Wang (Philosophy & Technology 35, 2022) introduces a Foucauldian power account of algorithmic transparency. This short commentary explores when this power account is appropriate. It is first observed that the power account is a constructionist one, and that such accounts often come with both factual and evaluative claims. In an instance of Hume’s law, the evaluative claims do not follow from the factual claims, leaving open the question of how much constructionist commitment (Hacking, 1999) one should have. The concept of acts in equilibrium (Nozick, 1981) is then used to explain how different individuals reading Wang can end up with different evaluative attitudes towards algorithmic transparency, despite factual agreement. The commentary concludes by situating constructionist commitment inside a larger question of how much to think of our actions, identifying conflicting arguments.

Pengaruh Stimulasi Tugas Terhadap Motivasi dan Pemahaman Membaca Mahasiswa Dengan Rancangan One Shot case study

This study seeks to increase intrinsic reading motivation by using situational interest to encourage the development of long-term individual reading motivation. Stimulating tasks are used to increase situational interest. Simultaneously, the researcher provides books on the topic of stimulating tasks to satisfy the curiosity arising from these tasks. Students who have high task stimulation show an increase in reading comprehension after controlling for initial comprehension. Students' reading motivation predicts the level of reading comprehension after controlling for initial comprehension. Task stimulation in reading increases situational interest, which increases long-term intrinsic motivation and reading comprehension.

Quick Generation of SSD Performance Models Using Machine Learning

Increasing usage of <i>Solid-State Drives</i> (SSDs) has greatly boosted the performance of storage backends. SSDs perform many internal processes such as out-of-place writes, wear-leveling, and garbage collection. These operations are complex and not well documented which make it difficult to create accurate SSD simulators. Our survey indicates that aside from complex configuration, available SSD simulators do not support both <i>sync</i> and <i>discard</i> requests. Past performance models also ignore the long term effect of I/O requests on SSD performance, which has been demonstrated to be significant. In this article, we utilize a methodology based on machine learning that extracts history-aware features at low cost to train SSD performance models that predict request response times. A key goal of our work is to achieve real-time or near-real time feature extraction and to achieve practical training times so our work can be considered as part of solutions that perform online or periodical characterization such as adaptive storage algorithms. Thus, we extract features from individual read, write, <i>sync</i> , and <i>discard</i> I/O requests and use structures such as exponentially decaying counters to track past activity using <inline-formula><tex-math notation="LaTeX">$O(1)$</tex-math></inline-formula> memory and processing cost. To make our methodology accessible and usable in real-world online scenarios, we focus on machine learning models that can be trained quickly on a single machine. To massively reduce processing and memory cost, we utilize feature selection to reduce feature count by up to 63%, allowing a feature extraction rate of 313,000 requests per second using a single thread. Our dataset contains 580M requests taken from 35 workloads. We experiment with three families of machine learning models, a) decision trees, b) ensemble methods utilizing decision trees, and c) <i>Feedforward Neural Networks</i> (FNN). Based on these experiments, FNN achieves an average <inline-formula><tex-math notation="LaTeX">$R^2$</tex-math></inline-formula> score of 0.72 compared to 0.61 and 0.45 for the Random Forest and Bagging, respectively, where <inline-formula><tex-math notation="LaTeX">$R^2 \in (-\inf, 1)$</tex-math></inline-formula> of 1 indicates a perfect fit. However, while the random forest model has lower accuracy, it uses general processing hardware and can be trained much faster, making it viable for use in online scenarios.

Novel Reading as Aesthetic: The Nesting of Aesthetic Experiences and Reproduction of Aesthetic Perception

Abstract This article discusses the nesting of the individual aesthetic experience and the reproduction process of aesthetic perception when an individual reads a novel. The essence of the “boundary” of the novelistic space is discussed first. This aesthetic process examines the relationship with the boundary of novelistic space. Next, I discuss two cognitive and dynamic outcomes that arise from the stimulation of “intervention” during the nesting of aesthetic experiences inside and outside the boundary. Finally, I argue that the reproduction process of aesthetic perception usually comes in the form of the “co-construction of opposites” due to the nesting of aesthetic experiences. This structure will make each individual's aesthetic experience distinctive and unique. In this research, a new viewpoint for reference will also be provided to research the arts’ aesthetic process in other forms.

User Perception and Eye Movement on A Pandemic Data Visualization Dashboard.

This study utilized a two-phase user experiment to explore people's perceptual and cognitive states interacting with the COVID-19 dashboard to obtain outbreak information. Specifically, 27 participants were assigned to interact with this dashboard with different color arrangements and performed image-memory, search, and browse visualization tasks sequentially. We found that the participants expected to obtain both global pandemic trends and single region/date statuses from the dashboard to help them grasp important information in the shortest possible time. They also allocated their attention differently to the dashboard's content areas to match their individual visual movement and reading logics. Our participants indicated that the pandemic data visualization dashboard should use a principal-color selection that is alarming but without causing panic. In the study's second phase, an eye-tracking experiment, it was found that the participants' actual eye paths deviated from our expectations: clustering around headings and text, rather than on visualized charts or graphs as anticipated. Based on these findings, we provide design implications for builders of future data-visualization and disaster dashboards.

Reading Strategies of Male and Female Pakistani ESL Undergraduates in the Context of Reading Indigenized Academic Texts

This study explores differences between 110 male and female Pakistani ESL undergraduates of a southern Punjab university as regard to their MCAP of reading strategies in the context of reading indigenized academic texts in English. MARSI was employed as the main instrument for data collection in this study. Collected data were analyzed through SPSS version 22. T-tests were conducted. Findings reveal that male and female ESL Learners gave mixed responses as far as their MCAP of individual reading strategies related to each subscale was concerned. However, females as compared to the males showed better response in collective strategy use for each of the three subscales of MARSI as well as for overall reading strategies (ORS). In the end, some recommendations were made by the researcher for future research in relation to the domain of metacognitive awareness of reading strategies for ESL Learners.

DETexT: An SNV detection enhancement for low read depth by integrating mutational signatures into TextCNN.

Detecting SNV at very low read depths helps to reduce sequencing requirements, lowers sequencing costs, and aids in the early screening, diagnosis, and treatment of cancer. However, the accuracy of SNV detection is significantly reduced at read depths below ×34 due to the lack of a sufficient number of read pairs to help filter out false positives. Many recent studies have revealed the potential of mutational signature (MS) in detecting true SNV, understanding the mutational processes that lead to the development of human cancers, and analyzing the endogenous and exogenous causes. Here, we present DETexT, an SNV detection method better suited to low read depths, which classifies false positive variants by combining MS with deep learning algorithms to mine correlation information around bases in individual reads without relying on the support of duplicate read pairs. We have validated the effectiveness of DETexT on simulated and real datasets and conducted comparative experiments. The source code has been uploaded to https://github.com/TrinaZ/extra-lowRD for academic use only.

Favored single nucleotide variants identified using whole genome Re-sequencing of Austrian and Chinese cattle breeds

Cattle have been essential for the development of human civilization since their first domestication few thousand years ago. Since then, they have spread across vast geographic areas following human activities. Throughout generations, the cattle genome has been shaped with detectable signals induced by various evolutionary processes, such as natural and human selection processes and demographic events. Identifying such signals, called selection signatures, is one of the primary goals of population genetics. Previous studies used various selection signature methods and normalized the outputs score using specific windows, in kbp or based on the number of SNPs, to identify the candidate regions. The recent method of iSAFE claimed for high accuracy in pinpointing the candidate SNPs. In this study, we analyzed whole-genome resequencing (WGS) data of ten individuals from Austrian Fleckvieh (Bos taurus) and fifty individuals from 14 Chinese indigenous breeds (Bos taurus, Bos taurus indicus, and admixed). Individual WGS reads were aligned to the cattle reference genome of ARS. UCD1.2 and subsequently undergone single nucleotide variants (SNVs) calling pipeline using GATK. Using these SNVs, we examined the population structure using principal component and admixture analysis. Then we refined selection signature candidates using the iSAFE program and compared it with the classical iHS approach. Additionally, we run Fst population differentiation from these two cattle groups. We found gradual changes of taurine in north China to admixed and indicine to the south. Based on the population structure and the number of individuals, we grouped samples to Fleckvieh, three Chinese taurines (Kazakh, Mongolian, Yanbian), admixed individuals (CHBI_Med), indicine individuals (CHBI_Low), and a combination of admixed and indicine (CHBI) for performing iSAFE and iHS tests. There were more significant SNVs identified using iSAFE than the iHS for the candidate of positive selection and more detectable signals in taurine than in indicine individuals. However, combining admixed and indicine individuals decreased the iSAFE signals. From both within-population tests, significant SNVs are linked to the olfactory receptors, production, reproduction, and temperament traits in taurine cattle, while heat and parasites tolerance in the admixed individuals. Fst test suggests similar patterns of population differentiation between Fleckvieh and three Chinese taurine breeds against CHBI. Nevertheless, there are genes shared only among the Chinese taurine, such as PAX5, affecting coat color, which might drive the differences between these yellowish coated breeds, and those in the greater Far East region.

A comprehensive comparison of facial skin hydration based on capacitance and conductance measurements in Chinese women.

The aim of this study was to compare the data of conductance and capacitance measurements of facial skin hydration and to evaluate and discuss the advantages and disadvantages of the different approaches. We measured skin capacitance (Corneometer® CM 825) and skin conductance (Skicon-200EX®) on 30 pre-defined facial sites of 125 Chinese women, resulting in 3750 readings per device. The data were analysed and compared, and continuous colour maps were generated on a 3D avatar for capacitance, conductance, relative difference (Δ%) and correlation (R-value) by interpolating between the individual readings and converting the values to colours. This visualization allows a better interpretation of the results. The complexity of facial skin hydration is revealed by this approach. The similarities and discrepancies in the facial hydration maps are clearly apparent. Due to the superiority of the Skicon in measuring high hydration levels, differences in skin hydration were evident on the forehead compared with the Corneometer maps, which may be related to the more superficial measurement of the Skicon within the stratum corneum. Conversely, a greater understanding of the complexity of facial skin hydration in the nasolabial fold was obvious when using the Corneometer. The best congruence between the instruments was found at two specific but separated facial areas, one around the inner eye region and the other one on a line between the nasolabial sulcus and the oblique, lateral jaw. Interestingly, the data were not normally distributed for both instruments and they had opposite skews. All facial clusters were statistically different from each other (p< 0.001), except the cheek and jaw for the Skicon. Larger than expected percentage coefficients of variance were found for the Corneometer on some facial sites that might be explainable by differences in stratum corneum physiology and biochemistry. Corneometer values of 48 AU and Skicon values of 132 μS were taken as the cutoff for normally hydrated facial skin. Both devices have their advantages and disadvantages suggesting that bio-instrumental measurement of skin hydration is actually more complicated than commonly thought and that the different facial zones and the use of multiple instrumentation have not been adequately considered.

Functional connectivity during orthographic, phonological, and semantic processing of Chinese characters identifies distinct visuospatial and phonosemantic networks.

While neuroimaging studies have identified brain regions associated with single word reading, its three constituents, namely, orthography, phonology, and meaning, and the functional connectivity of their networks remain underexplored. This study examined the neurocognitive underpinnings of these neural activations and functional connectivity of the identified brain regions using a within‐subject design. Thirty‐one native Mandarin speakers performed orthographic, phonological, and semantic judgment tasks during functional magnetic resonance imaging. The results indicated that the three processes shared a core network consisting of a large region in the left prefrontal cortex, fusiform gyrus, and medial superior frontal gyrus but not the superior temporal gyrus. Orthographic processing more strongly recruited the left dorsolateral prefrontal cortex, left superior parietal lobule and bilateral fusiform gyri; semantic processing more strongly recruited the left inferior frontal gyrus and left middle temporal gyrus, whereas phonological processing more strongly activated the dorsal part of the precentral gyrus. Functional connectivity analysis identified a posterior visuospatial network and a frontal phonosemantic network interfaced by the left middle frontal gyrus. We conclude that reading Chinese recruits cognitive resources that correspond to basic task demands with unique features best explained in connection with the individual reading subprocesses.

Across Textual Landscapes: The Role of Affect During Digital Reading Encounters

This article addresses questions related to how the change in the textual landscape, from paper-based books to electronic books, has an effect on the teaching of reading in early childhood classrooms as well as how the digital devices relate to different aspects of reading instruction. Drawing on the theoretical concept of affect, the purpose is to expand knowledge about processes of experiencing literary digital texts that are enacted and produced in a Swedish classroom when the teacher and the six-year-old students encounter digital narrative texts. The study draws on ethnographical methods to collect empirical material using video recording, field notes, and small interviews with children. The documentation includes both individual and collaborative reading of digital narratives. Discussed in the intersection between envisionment and affect, the results show that e-book activities create multiple and differing processes of reading. The metacognitive processes initiated by the teacher’s instruction of reading strategies create a distance between the student and the text, while processes of embodied sense-making create a closeness to the text that seems to be vital when the students encounter digital narratives and text worlds. These findings may contribute to educational as well as edu-political discussions about pedagogical rationales for e-book activities in which the dynamic and essential relation between body, space, and reading is made prominent.

The Microbial Community in the Abscess Underneath the Skin of Goats

The abscess underneath the skin is a common disease, which seriously affects the quality and yield of goat breeding. The main pathogens that cause abscesses are well understood, but the microbial community yet remains relatively unexplored. To determine the population and diversity of the microorganisms in the abscess underneath the skin of goats, in this work, 5 pus samples randomly collected from different goat farms (Jiangsu Province, China) were subjected to metagenomics sequencing and bioinformatics analysis. The test data show that the microbial communities of each sample contain about 79~82 kinds of microorganisms. Interestingly, each sample contained similar microbial species, including 53~59 kinds of bacteria, 5~6 fungi, 3 viruses, and 16~18 parasites. The top 5 dominant bacteria are Staphylococcus aureus, Lactococcus garvieae, Helicobacter pylori, Streptococcus pneumoniae, and Klebsiella pneumoniae, with an average abundance value of 29.88 %, 8.2%, 6.16%, 3.5%, and 3.26%, respectively. The remaining microbial abundances ranged from 0.01% to 3%. Although each of these frequent microorganisms is a tiny part of the total community, they constitute a major portion of individual reads (~1/2). In the conclusion, Staphylococcus aureus is the most dominant but nonunique bacterium responsible for the abscess underneath the skin of the goat, and the microbial community in the subcutaneous abscess is highly diverse. Bacterial coinfection should play an important role.