bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manufacturing Novel Textile Wearables Through Kirigami-Inspired Computerized Embroidery Stitching
Authors: Bisram Marisa , Wu Yunyun , Chen Kevin , Cao Jian 
Published: August 2024

Abstract
Textile manufacturing has seen remarkable advancements through the years in output speed and automation. Traditional approaches to crafting wearables a laminated composites from reinforcement rely on joining various textile pieces cut from a larger stock material together, a laborious and time-consuming process with high waste. In recent years, the introduction of seamless 3D knitting has been a revolutionary leap in this field, as it allows for a full structure without additional joining; however, it is not without its limitations with complex software and infrastructure requirements. The challenge that manufacturers now face is developing an easily accessible alternative to sustainable production of textiles. In this paper, we propose a novel method of fiber reinforcement and 3D wearable construction using kirigami inspired embroidery stitches. Advanced kirigami approaches coupled with digital embroidery technology allow for highly customizable textiles that can be optimized to form into varying shapes and stiffnesses. This work introduces a process for manufacturing embroidery-based textiles using kirigami patterns. Experimental testing occurs to understand the tensile mechanics of the structure as kirigami slits are included in the design, creating a foundation so that further optimization of the process can occur.
Time spent on active learning activities does not necessarily correlate with student exam performance: a controlled case study
Authors: Cen Xinjian , Lee Rachel J. , Contreras Christopher , Owens Melinda T. , Maloy Jeffrey 
Published: August 2024

ABSTRACT

Active learning, including student thinking and discussion in class, has been shown to increase student learning gains. However, it is less clear how instructor-level variation in the implementation and timing of active learning activities affects student gains. Our study aims to investigate the extent to which the time spent on individual episodes of active learning activities influences student performance. We hypothesized that instructors who let students spend more time on peer discussion and individual thinking on practice problems associated with particular learning objectives would have better student exam scores on exam questions addressing those objectives. To test this hypothesis, we obtained a large data set of classroom recordings and student exam scores from an introductory biology course at a large 4-year university, where three instructors shared identical teaching materials and exams for different course offerings. Contrary to our hypothesis, although the three instructors spent significantly different amounts of time on episodes of thinking and peer discussion, there was no correlation between the total time spent on active learning activities and student performance on exam questions. Linear mixed-effects modeling of the effect of the length of episodes of student thinking and discussion on exam score found that in the context of shared instructional materials, the amount of course time spent on active learning activities did not reliably predict student performance on associated exam questions. This result held true even when only considering learning objectives with high variations in performance between offerings, difficult exam questions, or exam questions requiring higher-order thinking skills. Although our study was only conducted in one course, our results imply that time spent per individual episode of student thinking or peer discussion may not be the primary factor explaining the positive effects of active learning and that it may be worthwhile to explore other factors.
Enhancing student engagement with introductory microbiology and immunology topics using a novel board game
Authors: Rivard Rebecca S. 
Published: August 2024

ABSTRACT

In introductory microbiology courses for non-biology majors, it can be difficult to ensure that students gain a functional understanding of the interplay between the host immune system and an invading infectious agent. Immune Battle is a board game that allows students to explore pathogen evolution and the immune system’s response to incursions in a captivating way, leveraging battleship and worker placement styles of gameplay. Students play in teams as either a pathogenic microbe attempting to reproduce and transmit itself to new hosts or as the immune system trying to defend the host from infection. Immune Battle seeks to mimic real-world interactions between immune cells and microbes using board game mechanics. For example, students will quickly find that adaptive immune system actions are better at fighting off microbial incursions than innate immune actions but require more time to activate. In this way, Immune Battle reinforces student’s understanding of the immune system and pathogenic virulence in an exciting and interactive way that keeps them thinking about host defenses long after the end of the class period or exam. This board game is well suited for advanced high school courses and introductory college-level courses that have only limited time to cover the immune system and microbiology. Documents containing the necessary components of the board game (not including a six-sided die) are included in the supplemental materials, so educators can print out their own copies and use this board game in their classes with no cost to themselves or their students.
How students taking introductory biology experience the chemistry content
Authors: Mendez Lilyan , Rivera Angelita T. , Vasquez Izabella , Godínez Aguilar Alfonso , Owens Melinda T. , Meaders Clara L. 
Published: August 2024

ABSTRACT

Student experiences learning chemistry have been well studied in chemistry courses but less so in biology courses. Chemistry concepts are foundational to introductory biology courses, and student experiences learning chemistry concepts may impact their overall course experiences and subsequent student outcomes. In this study, we asked undergraduate students enrolled in introductory biology courses at a public R1 institution an open-response question asking how their experiences learning chemistry topics affected their identities as biologists. We used thematic analysis to identify common ideas in their responses. We found that while almost half of student respondents cited learning chemistry as having positive impacts on their experiences learning biology, students who struggled with chemistry topics were significantly more likely to have negative experiences learning biology. We also found significant relationships between prior chemistry preparation, student background, and the likelihood of students struggling with chemistry and negative experiences learning biology. These findings emphasize the impact of learning specific content on student psychosocial metrics and suggest areas for biology educators to focus on to support learning and alleviate student stress in introductory biology.
Afucosylated anti-EBOV antibody MIL77-3 engages sGP to elicit NK cytotoxicity
Authors: Zhang Yuting , Zhang Min , Wu Haiyan , Wu Xiaonan , Zheng Hang , Feng Junjuan , Wang Mianjing , Wang Jing , Luo Longlong , Xiao He , Qiao Chunxia , Li Xinying , Zheng Yuanqiang , Huang Weijin , Wang Youchun , Wang Yi , Feng Jiannan , Chen Guojiang 
Published: August 2024

ABSTRACT

MIL77-3 is one component of antibody cocktail that is produced in our lab and represents an effective regimen for animals suffering from Zaire Ebolavirus (EBOV) infection. MIL77-3 is engineered to increase its affinity for the FcγRIIIa (CD16a) by deleting the fucose in the framework region. The potential effects of this modification on host immune responses, however, remain largely unknown. Herein, we demonstrated that MIL77-3 recognized secreted glycoproptein (sGP), produced by EBOV, and formed the immunocomplex to potently augment antibody-dependent cytotoxicity of human peripheral blood-derived natural killer cells (pNKs), including CD56
dim
and CD56
bright
subpopulations, in contrast to the counterparts (Mab114, rEBOV548, fucosylated MIL77-3). Intriguingly, this effect was not observed when NK92-CD16a cell line was utilized and restored by the addition of beads-coupled or membrane-anchored sGP in combination with MIL77-3. Furthermore, sGP bound to unrecognized receptors on T cells contaminated in pNKs rather than NK92-CD16a cells. Administration of beads-coupled sGP/MIL77-3 complex in mice elicited NK activation. Overall, this work reveals an immune-stimulating function of sGP/MIL77-3 complex by triggering cytotoxic activity of NK cells, highlighting the necessity to evaluate the potential impact of MIL77-3 on host immune reaction in clinical trials.

IMPORTANCE

Zaire Ebolavirus (EBOV) is highly lethal and causes sporadic outbreaks. The passive administration of monoclonal antibodies (mAbs) represents a promising treatment regimen against EBOV. Mounting evidence has shown that the efficacy of a subset of therapeutic mAbs
in vivo
is intimately associated with its capacity to trigger NK activity, supporting glycomodification of Fc region of anti-EBOV mAbs as a putative strategy to enhance Fc-mediated immune effector function as well as protection
in vivo
. Our work here uncovers the potential harmful influence of this modification on host immune responses, especially for mAbs with cross-reactivity to secreted glycoproptein (sGP) (e.g., MIL77-3), and highlights it is necessary to evaluate the NK-stimulating activity of a fucosylated mAb engaged with sGP when a new candidate is developed.
Whole-genome sequencing of three ciprofloxacin-resistant
Salmonella
Reading (ST93) strains, an emerging
Salmonella
serovar in the poultry sector of Pakistan
Authors: Siddique Abubakar , Tauqeer Azka , Ali Amjad , Ahsan Aitezaz , Iqbal Sajid , Patel Ami , Moore Terence , Ganda Erika , Rahman Abdur 
Published: August 2024

ABSTRACT

In this study, we performed whole-genome sequencing of three ciprofloxacin-resistant
Salmonella
Reading strains isolated from poultry meat. Genomes of
S
. Reading strains contained an average of 4.81 Mbp size with 52.1% GC. The isolates exhibited

bla
OXA-10

,
aac
[
6′
]
-Iaa
,
aadA1
,
cmlA1
,
qnrS1
, and
tetA
resistance genes and
IncX1
and
IncX2
plasmids.
Complete genome sequence of
Streptococcus intermedius
strain XH2169
Authors: Zhang Yisha , Yao Yue , Zhao Feng , Yu Yunsong , Hua Xiaoting 
Published: August 2024

ABSTRACT

Here, we report the complete genome sequence of
Streptococcus intermedius
strain XH2169 isolated from a blood sample in China. The genome comprises a single circular chromosome with a length of 1,944,282 bp. It harbored 1,891 coding gene sequences, 16 rRNA genes, 60 tRNA genes, and 3 noncoding RNA genes.
Draft genome sequences of
Klebsiella
spp. isolated from produce and agricultural water in South Korea
Authors: Oh Kwang-Kyo , Cho Gyu-Sung , Franz Charles M. A. P. 
Published: August 2024

ABSTRACT

This report outlines the draft genome sequences of six
Klebsiella
spp. strains from South Korea’s agricultural produce and environments. Genome sizes ranged from 5.25 to 6.21 Mbp with 55.64% to 57.55% GC content. Each strain contained multiple plasmid sequences identified by PlasmidFinder, indicating significant antimicrobial resistance.
Complete genome sequence of
Pigmentibacter ruber
isolated from a human patient in Japan
Authors: Hayashi Masahiro , Niwa Ayumi , Yonetamari Jun , Muto Yoshinori , Yokoyama Sodai , Nakamura Motohiro , Yokobori Yuta , Ogawa Mizuki , Ichioka Rina , Kikuchi Ryosuke , Okura Hiroyuki , Ogura Shinji , Tetsuka Nobuyuki , Baba Hisashi , Tanaka Kaori 
Published: August 2024

ABSTRACT

Pigmentibacter ruber
is a newly described bacterium belonging to the Silvanigrellaceae family that was isolated from human blood in 2021. We report the complete genome sequence of a clinical isolate of
P. ruber
(GTC16762) obtained from a human patient in Japan. Its genome contains a 3.6-Mb chromosome and three circular plasmids.
Draft genome sequence of two
Fusobacterium varium
strains isolated from patients in Kazakhstan with colorectal cancer
Authors: Kurentay Botakoz , Gusmaulemova Alua , Utupov Talgat , Auganova Dana , Tarlykov Pavel , Daniyarov Asset , Khamzina Saule , Mamlin Meiram , Kozhakhmetov Arman , Shalekenov Sanzhar , Kulmambetova Gulmira 
Published: August 2024

ABSTRACT

Fusobacterium varium
is a Gram-negative, invasive, obligate anaerobe in the gastrointestinal tract microbiota, associated with various clinical conditions, including colorectal cancer (CRC). Here, we announce the draft genome sequence of two
F. varium
strains Fv36kaz and Fv63kaz from patients with CRC in Kazakhstan.
Draft genome sequence of
Amyloporia xantha
strain YAFMF0618, isolated from Gaoligong Mountain
Authors: Zhao Xiaolei , Yuan Xiaolong , Yin Yihang , Yu Jiaojun , Zheng Yuan , Wang Yi 
Published: August 2024

ABSTRACT

The
Amyloporia
genus is an important Chinese medicinal fungus. Here, we present a draft genome sequence of
Amyloporia xantha
strain YAFMF0618. The genome resource will support subsequent research into the potential secondary metabolite diversity of
A. xantha
.
Genome sequences of
Clostridium perfringens
isolated from diseased dogs
Authors: Sekse Camilla , Solsvik Helene K. , Haverkamp Thomas H. A. , Kaspersen Håkon , Gulliksen Wenche S. , Campos Sabrina R. , Nørstebø Simen F. , Bøe Cathrine A. 
Published: August 2024

ABSTRACT

Two
Clostridium perfringens
isolates originating from two Norwegian dogs with acute hemorrhagic diarrhea were sequenced. Based on Illumina and Oxford Nanopore Technology sequencing, hybrid assemblies were generated, and one of the genomes was completed and closed. For both isolates, virulence genes and their genomic location have been identified.
Detection of mobile colistin resistance genes
mcr-9.1
and
mcr-10.1
in
Enterobacter asburiae
from Ecuadorian children
Authors: Cifuentes Sara G. , Graham Jay , Trueba Gabriel , Cádenas Paúl A. 
Published: August 2024

ABSTRACT

Colistin is one of the last-line treatments for multi-drug resistant Gram-negative bacterial infections. The emergence of mobile colistin resistance genes has driven global concern and triggered the need for surveillance. Our report reveals the identification of
mcr-9.1
and
mcr-10.1
in Ecuador by employing a proximity ligation technique.
Complete genome sequence of the OXA-48-producing
Klebsiella pneumoniae
strain 11978
Authors: Raro Otávio Hallal Ferreira , Nordmann Patrice , Poirel Laurent 
Published: August 2024

ABSTRACT

We announce the complete genome sequence of
Klebsiella pneumoniae
strain 11978 isolated from a patient hospitalized in Turkey in 2001. The genome belongs to sequence type 14 and includes three plasmids. Notably, it presents an IncL plasmid carrying
bla
OXA-48
, which demonstrated global success in terms of dissemination.
Complete genome sequence of a
Salimicrobium
sp. PL1-032A isolated from the pink hypersaline Pearse Lakes, Rottnest Island, Western Australia
Authors: Young Crystal E. , Alattas Hussain , Scott Colin , Murphy Daniel V. , Tiwari Ravi , Reeve Wayne G. 
Published: August 2024

ABSTRACT

Salimicrobium
sp. PL1-032A was isolated from Pearse Lakes, Western Australia. The sequenced genome consists of a single chromosome (2,705,688  bp) with a GC content of 47.2%. The isolation of
Salimicrobium
sp. PL1-032A contributes to the collection of culturable extremophiles and offers potential insight into the Pearse Lakes biome.
Whole-genome sequencing of
Enterococcus faecalis
probiotic strains isolated from raw milk of healthy cows
Authors: Rahman Md. Morshedur , Siddique Naim , Rahman ANM Aminoor , Das Ziban Chandra , Islam Tofazzal , Hoque M. Nazmul 
Published: August 2024

ABSTRACT

We report the draft genomes of two
Enterococcus faecalis
strains MBBL1 and MBBL2, isolated from raw milk of healthy cows. The genome of MBBL1 is 2,681,695 bp with 57.41× coverage, and MBBL2 is 2,681,119 bp with 99.81× coverage, spanned across 14 and 13 contigs, respectively.
Draft genome for
Flavobacterium psychrophilum
isolates from diseased coho salmon (
Oncorhynchus kisutch
) in Chile
Authors: Avendaño-Herrera Ruben , Saldarriaga-Córdoba Mónica , Ilardi Pedro 
Published: August 2024

ABSTRACT

We present the draft genome sequences of six
Flavobacterium psychrophilum
isolates recovered from diseased coho salmon (
Oncorhynchus kisutch
) cultured by two farms in Chile. This study provides the first detailed insights into the genomic characteristics of this fish pathogen recovered from a host with limited information and cultured in Chile.
Report of SARS-CoV-2 JN.1 variant in Morocco
Authors: Bouddahab Oumaima , El Hamouchi Adil , Aqillouch Safaa , Charoute Hicham , Noureddine Rachid , Aainouss Achraf , Baba Hanâ , Ouladlahsen Ahd , Nourlil Jalal , Sarih M'hammed , Maaroufi Abderrahmane , Lkhider Mustapha , Barakat Abdelhamid , Ezzikouri Sayeh 
Published: August 2024

ABSTRACT

In this study, we report the identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) JN.1 variant and the quasi-complete genomic sequencing of four clinical samples in Morocco. Nasopharyngeal swabs were obtained from four patients (one female, three males). The Illumina COVIDSeq Test was used for comprehensive genomic analysis.
Complete genomic sequence of a
Marinobacter
species, a potential polyethylene degrader isolated from surface seawater
Authors: Iizuka Ryo , Uemura Sotaro 
Published: August 2024

ABSTRACT

The bacterium
Marinobacter
sp. RI1 was isolated from surface seawater through an enrichment culture using low-density polyethylene as the sole carbon source. Herein, we report its complete genomic sequence. Genomic annotation revealed that the strain harbors the genes encoding enzymes involved in alkane degradation, thus supporting polyethylene degradation.
Mapping disparities in viral infection rates using highly multiplexed serology
Authors: Piña Alejandra , Elko Evan A. , Caballero Rachel , Metrailer Morgan , Mulrow Mary , Quan Dan , Nordstrom Lora , Altin John A. , Ladner Jason T. 
Published: August 2024

ABSTRACT

Despite advancements in medical interventions, the disease burden caused by viral pathogens remains large and highly diverse. This burden includes the wide range of signs and symptoms associated with active viral replication as well as a variety of clinical sequelae of infection. Moreover, there is growing evidence supporting the existence of sex- and ethnicity-based health disparities linked to viral infections and their associated diseases. Despite several well-documented disparities in viral infection rates, our current understanding of virus-associated health disparities remains incomplete. This knowledge gap can be attributed, in part, to limitations of the most commonly used viral detection methodologies, which lack the breadth needed to characterize exposures across the entire virome. Additionally, virus-related health disparities are dynamic and often differ considerably through space and time. In this study, we utilize PepSeq, an approach for highly multiplexed serology, to broadly assess an individual’s history of viral exposures, and we demonstrate the effectiveness of this approach for detecting infection disparities through a pilot study of 400 adults aged 30–60 in Phoenix, AZ. Using a human virome PepSeq library, we observed expected seroprevalence rates for several common viruses and detected both expected and previously undocumented differences in inferred rates of infection between our male/female and Hispanic/non-Hispanic White individuals.

IMPORTANCE
Our understanding of population-level virus infection rates and associated health disparities is incomplete. In part, this is because of the high diversity of human-infecting viruses and the limited breadth and sensitivity of traditional approaches for detecting infection events. Here, we demonstrate the potential for modern, highly multiplexed antibody detection methods to greatly increase our understanding of disparities in rates of infection across subpopulations (e.g., different sexes or ethnic groups). The use of antibodies as biomarkers allows us to detect evidence of past infections over an extended period, and our approach for highly multiplexed serology (PepSeq) allows us to measure antibody responses against hundreds of viruses in an efficient and cost-effective manner.
Cultivation in long-term simulated microgravity is detrimental to pyocyanin production and subsequent biofilm formation ability of
Pseudomonas aeruginosa
Authors: Chen Kenny Zhi Ming , Vu Linda My , Vollmer Amy Cheng 
Published: August 2024

ABSTRACT

Pseudomonas aeruginosa
forms aggregates known as biofilms. Previous studies have shown that when
P. aeruginosa
is cultivated in space, thicker and structurally different biofilms are formed than from those grown on Earth. We investigated how microgravity, simulated in a laboratory setting, influenced the growth, colonization, and virulence potentials of a
P. aeruginosa
PA14 wild-type strain, as well as two surface attachment-defective (
sad
) mutants altered at crucial biofilm-forming steps:
flgK
and
pelA
. Using high-aspect ratio rotating-wall vessel (HARV) bioreactors,
P. aeruginosa
bacteria were grown to stationary phase under prolonged (6 days) exposure to simulated microgravity or normal gravity conditions. After the exposure, the capacity of the culture to form biofilms was measured. Additionally, pigment (pyocyanin) formed by each culture during the incubation was extracted and quantified. We demonstrate that the first prolonged exposure to low-shear modeled microgravity (LSMMG) and without nutrient replenishment significantly diminishes wild-type
P. aeruginosa
PA14 biofilm formation abilities after exposure and pyocyanin production during exposure, while the mutant strains exhibit differing outcomes for both properties.

IMPORTANCE

Given plans for humans to engage in prolonged space travel, we investigated biofilm and pigment/virulence factor formation in
Pseudomonas aeruginosa
when cultivated in microgravity. These bacteria are opportunistic pathogens in immunocompromised individuals. Previous studies of space travelers have shown some immune system diminutions. Hence, our studies shed some light on how prolonged cultivation of bacteria in simulated microgravity conditions affect their growth characteristics.