bluuebunny/crossref_metadata_2025 huggingface dataset:
Perspectives of South Asian Youth in the United States about Gender Norms and Healthcare Decision Making
Authors: Khosla Nidhi , Bhandari Shreya
Published: July 2024

The aim of this study was to explore the voices of South Asian youth in the United States about gender norms and healthcare decision making. Ten focus group discussions were held with 36 students of South Asian origin at a university on the West Coast of the United States. Thematic analysis was performed on the focus group data. Three main themes emerged from the data: (1) intersectionality of gender with other factors that affect healthcare decision making, (2) impact of gender on health, and (3) coping strategies. Participants reported preferential treatment for boys versus girls, vesting decision-making control among males, worse health among females, and coping strategies. A few responses indicated that power differentials in some families were shifting to a more egalitarian balance between males and females. Aspects such as age, employment, and language barriers intersected with gender to create a complex web of influence on healthcare decision making. The study has implications for social workers to offer culturally responsive support to South Asian youth in the United States, paying attention to the intersectionalities when working with them. Further research is needed to explore the influence of gender on healthcare decision-making processes of South Asian youth in the United States.
Valtrate Suppresses TNFSF14-Mediated Arrhythmia After Myocardial Ischemia–Reperfusion by Inducing N-linked Glycosylation of LTβR to Regulate MGA/MAX/c-Myc/Cx43
Authors: Zhang Jing , Xiong Xiaoqi , Li Jun , Luo Changjun , Su Qiang , Hao Xin , Wu Qiang , Huang Wanzhong
Published: July 2024

Myocardial ischemia–reperfusion (MIR)-induced arrhythmia remains a major cause of death in patients with cardiovascular diseases. The reduction of Cx43 has been known as a major inducer of arrhythmias after MIR, but the reason for the reduction of Cx43 remains largely unknown. The aim of this study was to find the key mechanism underlying the reduction of Cx43 after MIR and to screen out an herbal extract to attenuate arrhythmia after MIR. The differentially expressed genes in the peripheral blood mononuclear cell (PBMCs) after MIR were analyzed using the data from several gene expression omnibus data sets, followed by the identification in PBMCs and the serum of patients with myocardial infarction. Tumor necrosis factor superfamily protein 14 (TNFSF14) was increased in PBMCs and the serum of patients, which might be associated with the injury after MIR. The toxic effects of TNFSF14 on cardiomyocytes were investigated in vitro. Valtrate was screened out from several herbal extracts. Its protection against TNFSF14-induced injury was evaluated in cardiomyocytes and animal models with MIR. Recombinant TNFSF14 protein not only suppressed the viability of cardiomyocytes but also decreased Cx43 by stimulating the receptor LTβR. LTβR induces the competitive binding of MAX to MGA rather than the transcriptional factor c-Myc, thereby suppressing c-Myc–mediated transcription of Cx43. Valtrate promoted the N-linked glycosylation modification of LTβR, which reversed TNFSF14-induced reduction of Cx43 and attenuated arrhythmia after MIR. In all, valtrate suppresses TNFSF14-induced reduction of Cx43, thereby attenuating arrhythmia after MIR.
Dynamic Changes in Segmented Neutrophil-to-Monocyte Ratio in Trauma Patients with Stress-Induced Hyperglycemia: A Retrospective Study
Authors: Huang Ching-Ya , Hsu Shiun-Yuan , Tsai Ching-Hua , Su Wei-Ti , Lin Ko-Chien , Hsieh Ching-Hua
Published: July 2024

Introduction

Stress-induced hyperglycemia (SIH) is commonly observed in patients with trauma and is associated with increased morbidity and mortality. The segmented neutrophil-to-monocyte ratio (SeMo) serves as a biomarker of inflammation and potentially reflects the severity of the stress response to trauma. This study investigated the relationships between SIH, dynamic changes in SeMo, and patient outcomes in a trauma intensive care unit (ICU).

Methods

A retrospective analysis was conducted using data from adult patients with trauma admitted to a Level I trauma center in Southern Taiwan over 13 years. Patients were divided into two groups based on the presence of SIH or non-diabetic normoglycemia (NDN). The dynamic SeMo was calculated as the difference in the SeMo from admission to 48-72 hours after admission. Outcomes were compared using descriptive statistics, chi-square tests, and Student's t-tests.

Results

Of the 1,030 included patients, those with SIH had a significantly higher SeMo (20.3 vs. 15.2, P = 0.001) and a greater change in dynamic SeMo (1.2 vs. -4.0, P = 0.017) than those with NDN. Among patients with SIH, the deceased group had a higher SeMo (26.4 vs. 18.4, P = 0.022), but there was no difference in dynamic SeMo among the survivors. In the overall cohort and the NDN subgroups, dynamic SeMo was not associated with mortality. However, factors such as older age, lower Glasgow Coma Scale score, higher Injury Severity Score, and presence of end-stage renal disease were more strongly associated with increased mortality.

Conclusion

In patients with trauma in ICU, SIH was linked to an increased SeMo and greater changes in dynamic SeMo; however, these changes did not directly predict mortality. It is important to note that an elevated SeMo may be observed in patients with SIH, but not in patients with NDN. This finding should be considered to avoid unnecessary therapies.
Aesthetic and Functional Reconstruction of Periorbital Region Using Radial Forearm Free Flap
Authors: Chaiyasate Kongkrit , Abdul-hamed Senan , Lohasammakul Suphalerk
Published: July 2024

Background:

This study describes the utilization of the radial forearm free flap (RFFF) for the restoration of severe soft tissue deficiency involving the upper and lower eyelids in three patients.

Methods:

This study is a retrospective review of the senior authors’ clinical records for patients who presented with periorbital defect and underwent reconstruction with RFFF between 2018 and 2022.

Results:

As a part of a comprehensive reconstructive surgery, we used the RFFF to deliver an ample amount of well-vascularized soft tissue. The flap’s vessels were anastomosed to the ipsilateral facial vessels in all cases. Patients showed significant functional improvement, with complete eyelid closure achieved. No immediate postoperative complications were noted.

Conclusions:

RFFF demonstrated optimal outcomes in upper eyelid reconstruction.
TSG-6 Is Involved in Fibrous Structural Remodeling after the Injection of Adipose-derived Stem Cells
Authors: Kiuchi Satomi , Lopes Tiago J.S. , Oishi Takaya , Cho Yuki , Ochiai Hiroko , Gomi Takamasa
Published: July 2024

Background:

Although aesthetic treatments can rejuvenate the skin, they often cause specific forms of tissue damage. Unlike wounding, which typically results in fibrotic scar tissue, damage from aesthetic treatments induces a distinct histological rejuvenation. The mechanisms that drive this rejuvenation are not yet fully understood. Here, we were interested in cellular responses following aesthetic treatments injecting adipose-derived stem cells (ASCs) subcutaneously. Through investigation with an ex vivo experimental model, a key gene was identified that orchestrates fibrous structural changes and tissue remodeling.

Methods:

Using fresh human subcutaneous adipose tissue co-cultured with ASCs, the changes in the fibrous architecture of the tissue were sequentially mapped. The key regulatory genes involved in remodeling were identified using gene expression and computational analyses.

Results:

We identified the regulatory elements that are crucial for tissue remodeling. Among those, we found that tumor necrosis factor-stimulated gene-6 (TSG-6) is a paracrine mediator essential for the collagen activity. It not only alleviates tissue inflammation but also promotes collagen replacement ex vivo. This is primarily achieved by inhibiting the formation of neutrophil extracellular traps, which are known to promote fibrosis.

Conclusions:

TSG-6 is a key factor modulating tissue inflammation. As our results demonstrate, after ASCs treatment, this factor directs skin healing away from fibrosis by reducing neutrophil extracellular trap formation in subcutaneous adipose tissue and promotes fibrous rejuvenation.
Does Soaking Fresh Frozen Costal Cartilage in an Antibiotic Solution Reduce Postoperative Infection in Rhinoplasty?
Authors: Datta Shaishav , Mattos David , Hanna Steven A. , Reish Richard G.
Published: July 2024

Background:

Fresh frozen costal cartilage (FFCC), from the Musculoskeletal Transplant Foundation (MTF), has recently gained popularity for use in revision rhinoplasty or primary rhinoplasty when there is a paucity of autologous cartilage. However, there are currently no guidelines related to the use of intraoperative antibiotic soaking to reduce postoperative infection rates when using MTF FFCC. This study aimed to evaluate the efficacy of intraoperative antibiotic soaks in reducing surgical site infection rate when using MTF FFCC grafts in rhinoplasty.

Methods:

A retrospective chart review of patients who underwent rhinoplasty with the use of MTF FFCC in the senior author’s practice was conducted between May 2017 and June 2022. The inclusion criteria were rhinoplasty cases using MTF FFCC with minimum of 12 months of follow-up. Fisher exact test was conducted to determine significance in rates of postoperative infection for patients who underwent rhinoplasty with the use of MTF FFCC with (1) intraoperative antibiotic solution soak versus (2) no antibiotic solution soak.

Results:

A total of 310 patients were included and separated into two cohorts, MTF FFCC intraoperative antibiotic solution soak (n = 200) and no antibiotic solution soak (n = 110). There were a total of four (1.3%) cases of infection, all in the antibiotic soak group. There was no statistically significant difference between the rate of infection in the two cohorts (P = 0.301).

Conclusion:

Our retrospective cohort study demonstrates that soaking MTF FFCC in an antibiotic solution intraoperatively does not reduce postoperative infection rates in rhinoplasty.
Updates to the Physiologic Mechanism, Anatomical Sites, and Diagnostic Utility of the Scratch Collapse Test: A Systematic Review
Authors: Faszholz Alicia M , Cheng Jonathan
Published: July 2024

Background:

The scratch collapse test (SCT) has gained popularity as a physical examination technique for diagnosing compression neuropathy. This systematic review aims to assess the reliability of the SCT as a diagnostic tool for compression neuropathy, as well as to propose the underlying physiological mechanisms involved. Specific criteria was developed to broaden the potential anatomical applications of the SCT.

Methods:

A literature search was conducted using PubMed, Embase, Scopus, and Google Scholar. Eleven articles meeting predefined inclusion/exclusion criteria were selected for numerical analysis, which yielded sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy values.

Results:

In total, 890 patients with carpal tunnel syndrome were reported in 10 studies. The mean (±SD) sensitivity, specificity, PPV, NPV, and accuracy were 0.442 ± 0.272, 0.788 ± 0.163, 0.834 ± 0.143, 0.433 ± 0.297, and 48.8% (range, 31%–82%), respectively. Of the studies that provided interrater reliability (κ), the mean was 0.544 ± 0.441, indicating moderate agreement. A total of 121 patients with cubital tunnel syndrome were reported in three studies, with a mean (±SD) sensitivity and specificity of 0.635 ± 0.367 and 0.945 ± 0.06, respectively. Twenty-four patients with peroneal nerve compression, reported in one study, had sensitivity, specificity, PPV, NPV, and accuracy of 0.77, 0.99, 0.95, 0.92, and 93%, respectively.

Conclusions:

Current literature indicates that the SCT can serve as a provocative test to assist in diagnosing compression neuropathy. Nevertheless, the heterogeneity of reported values underscores the necessity for further investigation aimed at enhancing the objectivity of SCT, thus improving interrater reliability and minimizing potential bias.
EXPLORING THE CHALLENGES OF DISTINGUISHING PUNCTATE INNER CHOROIDOPATHY FROM MULTIFOCAL CHOROIDITIS AND PANUVEITIS
Authors: Park Hyo Song , Kang Hyun Goo , Kim Yong Joon , Choi Eun Young , Lee Junwon , Byeon Suk Ho , Kim Sung Soo , Lee Christopher Seungkyu
Published: July 2024

Purpose:

This retrospective case series aimed to assess the concordance between clinical diagnoses of punctate inner choroidopathy and multifocal choroiditis and panuveitis (MCP) using the 2021 Standardization of Uveitis Nomenclature Working Group criteria.

Methods:

Using the medical records of the patients, the authors reevaluated 100 eyes of 75 patients with idiopathic multifocal chorioretinal inflammatory lesions based on Standardization of Uveitis Nomenclature criteria and compared the result with the clinical diagnosis.

Results:

Of 100 eyes, 29 eyes (29%) were diagnosed as punctate inner choroidopathy and 15 eyes (15%) were diagnosed as MCP using Standardization of Uveitis Nomenclature criteria, and 56 (56%) eyes could not be diagnosed as either. Clinically diagnosed punctate inner choroidopathy eyes were significantly more myopic than the clinically diagnosed MCP eyes (mean spherical equivalent −6.65 ± 4.63 vs. −3.85 ± 2.31, P = 0.01). Sixteen eyes with vitreous inflammation were all clinically diagnosed as MCP, but four (25%) could not be diagnosed as MCP using Standardization of Uveitis Nomenclature criteria.

Conclusion:

The existing diagnostic criteria showed limitations in capturing all clinical cases of punctate inner choroidopathy or MCP, and adding or revising criteria on features such as vitreous inflammation or myopia could be considered to enhance diagnostic accuracy.
Bilateral Central serous chorioretinopathy in a case of surgically treated Optic Disc Pit maculopathy
Authors: Kala Urvashi , Sen Ahana , Majumdar Bristi , Shambhawi Pragya , Juneja Aarzoo , Divya N Sai , Chowdhury Ruchira , Saurabh Kumar , Roy Rupak
Published: July 2024

Purpose:

To report occurrence of central serous chorioretinopathy(CSCR) which mimicked recurrence of ODP maculopathy in a young adult in whom surgery for the same had been done.

Methods:

Clinical fundus examination and multimodal imaging which included optical coherence tomography(OCT) and fundus autofluorescence(FFA) was done

Results:

Patient had undergone surgery for ODP maculopathy. At 1 year follow up, there was recurrence of subretinal fluid at the macula. Fundus fluorescein angiography was done and the presence of ink blot pattern leakage clinched the diagnosis of CSCR, ruling out ODP maculopathy.

Conclusion:

CSCR is a great masquerade and correct diagnosis is very important to prevent permanent visual impairment. Subretinal fluid(SRF) associated with ODP must be examined carefully to rule out other pathologies like CSCR. Serous macular detachment after surgery for ODP maculopathy has been done, does not necessarily mean recurrence of the maculopathy. Other pathologies like CSCR should be ruled out. This case highlights the importance of multimodal imaging along with clinical signs in correct diagnosis and treatment of conditions with overlapping features like CSCR and ODP maculopathy.
The effect of intrathecal pethidine on post-spinal anesthesia shivering after cesarean section: a systematic review and meta-analysis
Authors: Afzal Muhammad , Lee Amber , Asad Muhammad , Ali Alya , Farrukh Ameer Mustafa , Semakieh Bader , Levin-Carrion Yaxel , Shah Shah Rukh , Khan Qaisar Ali
Published: July 2024

Background:

Spinal anesthesia is the most preferred method for cesarean section (C-section). This meta-analysis was performed to determine the effect of low and high intrathecal doses of pethidine on the maternal outcomes after C-section.

Methods:

A systematic search of PubMed, Scopus, Cochrane Library, and Google Scholar was performed. Random-effects meta-analysis was performed to derive odds ratios (ORs) from dichotomous data.

Results:

Seventeen randomized controlled trials with 1304 C-section patients were included. Patients who had received intrathecal pethidine experienced decreased shivering and intensity of shivering (OR 0.13; P<0.001) and (OR 0.21; P<0.001), respectively. Moreover, vomiting (OR 2.47; P=0.002) and pruritus (OR 5.92; P<0.001) were significantly higher in the pethidine group. There was no statistically significant difference in the incidence of nausea (OR 2.55; P=0.06) and hypotension (OR 0.91; P=0.67).

Conclusions:

Intrathecal pethidine can effectively decrease shivering, although it increases the risk of vomiting and pruritus. No significant difference was found both in the maternal hypotension and nausea.
Vagus Nerve Stimulation Paired With Rehabilitation for Chronic Stroke: Characterizing Responders
Authors: Beovich Alexa , Boose Jessica , Patel Rachana , Wolf Steven L.
Published: July 2024

Background and purpose:

Implantable vagus nerve stimulation (VNS) paired with volitional upper extremity rehabilitation can improve impairment and function among moderately to severely impaired, chronic stroke survivors. This study is a retrospective analysis of the in-clinic rehabilitation phase of the blinded, placebo-controlled, randomized pivotal VNS-REHAB trial to determine whether dosing parameters during in-clinic paired VNS therapy were associated with responder status and whether covariates might impact that determination.

Methods:

Data were limited to 53 participants in the active VNS group who had received VNS implants prior to undergoing 6 weeks of in-clinic rehabilitation paired with VNS. Tasks were standardized across all participants. Dosing parameters included number of stimulations and task time. The primary outcome was the Fugl-Meyer Upper Extremity Assessment (FMA-UE), evaluated at the end of 6 weeks (Post-1). Participants were classified a priori as responders based on an improvement of ≥6 points on the FMA-UE from baseline to Post-1.

Results:

Dosing parameters were not associated with FMA-UE responder status at the end of 6 weeks. Covariates including age, gender, paretic hand, baseline severity, and chronicity of stroke were also not significant associations of response.

Discussion and Conclusions:

While responders to VNS could be defined, therapy dosing and participant attributes did not provide greater specification for association of responder status. Limitations of this study include small sample size and non-linearity of the FMA-UE. Future studies will include reassessing responder categorization using more linear scales and examining stroke lesion characteristics to determine whether these measures are more sensitive to dosing parameters.

Video Abstract available

for more insights from the authors (see the Video, Supplemental Digital Content 1, available at: http://www.w3.org/1999/xlink).
Risk Factors of Lymph Node Metastasis and Prognosis in 891 Chinese Patients With Submucosal Early Gastric Carcinoma, Emphasizing Differences Between Gastric Cardiac and Noncardiac Origins
Authors: Cheng Yuqing , Du Mingzhan , Wang Yaohui , Li Ting , He Chongfang , Zhou Xiaoli , Lin Min , Huang Qin
Published: July 2024

Differences in risk factors (RF) of lymph node metastasis (LNM) and prognosis between submucosal early gastric cardiac (SEGCC) and noncardiac (SEGNCC) carcinomas remain unclear. In this study, we investigated and compared RF of LNM and prognosis in 891 patients with radical gastrectomy for SEGCC (n=217) or SEGNCC (n=674). Compared with SEGNCC, SEGCC displayed significantly higher proportion of elderly patients (70 y or above), the elevated macroscopic type, well/moderately differentiated tubular and low-grade papillary adenocarcinomas, as well as low-grade tumor budding, but lower prevalence of the depressed macroscopic type, poorly differentiated tubular adenocarcinoma, mixed adenocarcinoma, poorly cohesive carcinoma, lymphovascular invasion (LVI), perineural invasion, and high-grade tumor budding. By univariate analysis, significant RF for LNM of the cohort included female sex, poor differentiation, SM2 invasion, LVI, intermediate-grade and high-grade tumor budding, whereas tumor size, histology type, and perineural invasion were the significant RF for LNM in SEGNCC. By multivariate analysis, significant independent RF for LNM included female sex and LVI in SEGCC but were female sex, mixed adenocarcinoma, LVI, and high-grade tumor budding in SEGNCC. The 5-year overall survival was significantly worse in SEGCC than in SEGNCC for patients with LNM, but not for those without. For overall survival, LNM was the only significant independent RF in SEGCC, whereas age 70 years or above and LNM were independent RF in SEGNCC. The results of our study provided the clinicopathologic evidence for individualized clinical management strategies for these 2 groups of patients and suggested different pathogenesis mechanisms between SEGCC and SEGNCC.
The Optimal Effective Dose of Adipose-Derived Stem Cell Exosomes in Wound Healing
Authors: Kemaloğlu Cemal Alper , Dursun Ece Nur , Yay Arzu Hanım , Gökdemir Nur Seda , Mat Özge Cengiz , Gönen Zeynep Burçin
Published: July 2024

Introduction

Although the effect of adipose-derived mesenchymal stem cell exosomes (ADSC-exos) on wound healing with different doses are shown in various studies, efficient and sufficient doses of ADSC-exos are still unknown. The study aimed to determine the optimal dose of ADSC-exos in wound healing.

Methods

The 45 Sprague-Dawley rats were randomly divided into five groups, with seven animals in each. After dorsal circular defects were created, each wound was injected as follows: group 1: saline, group 2: 10 μg/mL of ADSC-exos, group 3: 100 μg/mL of ADSC-exos, group 4: 200 μg/mL of ADSC-exos, and group 5: 400 μg/mL of ADSC-exos. The effects of ADSC-exos on epithelization, angiogenesis, and collagen formation were analyzed macroscopically, histopathologically, and immunohistochemically on day 14.

Results

A total of 200 μg/mL and 400 μg/mL ADSC-exos groups had higher epithelial tongue length, epithelial tongue area, and angiogenesis scores than the other groups. Although there was no statistical difference in fibrosis scores among groups, collagen fibers were becoming well-organized as the ADSC-exos doses increased. While the wound area was clinically smaller in the 200 μg/mL ADSC-exos group, there was no statistically significant difference among groups on day 14.

Conclusions

A total of 200 μg/mL of ADSC-exos was found to be the adequate and effective dose for re-epithelialization and angiogenesis in cutaneous wound healing. Moreover, the collagen density increased with a more regular pattern in the 200 μg/mL group, which can be important in scar regulation.
Physicochemical and textural properties of thawed pork by vacuum
tumbling
Authors: Park Su-Jin , Hong Won-Ho , Oh Seung-Min , Cho Chang-Hee , Chun Jiyeon
Published: July 2024

In this study, a vacuum tumbler with 4 impellers (DVT) was designed and applied
for thawing frozen pork (vacuum −60 kPa, jacket 35°C, 1 rpm).
Quality characteristics of the thawed pork were compared with those of
industrially thawed meat by natural air at room temperature (NAT) and imported
vacuum tumbler (IVT). The thawing time for frozen pork (303.36 kg) using DVT
(165 min) was much shorter than that of NAT (4,200 min). DVT-thawed pork had
lower drip loss (0.85%) than NAT (2.08%). DVT-thawed pork showed a
pH of 5.92, a total bacterial count of 1.96±0.02 log CFU/g and no
coliforms. Deteriorations in fat (TBARS 0.31±0.01 MDA mg/kg) and protein
(VBN 5.67±1.98 mg%) in DVT-thawed pork were significantly lower
than those of NAT (p<0.05). DVT-thawed pork had a high water-holding
capacity (WHC, 97.5%). The hardness (34.59±0.46 N) and chewiness
(188.21±0.17) of cooked DVT-thawed pork were about 5-6 times lower than
those of NTA. Microstructure (SEM) showed myofibrillar damage in NAT-thawed
pork, whereas dense myofibrillar structure was observed in DVT-thawed pork. DVT
was better or similar to IVT in all evaluation parameters. The designed DVT is
expected to be used as an efficient thawing method in terms of processing time
and yield and to produce thawed meat with high WHC, soft texture, and low
spoilage by minimizing tissue damage.
Effects of packaging method and root trimming on quality of green
onion (Allium fistulosum L.) during storage
Authors: Choi Ji Weon , Cho MiAe , Jung Ki-Sik , Cho Jae Han , Lee Ji Hyun , Lim Sooyeon
Published: July 2024

This study investigated the effect of packaging method and root trimming on
quality of green onions during storage. Two packaging methods (tied with string,
S or packaged with film bag, FP) and two root trimming states (attaching the
roots without trimming, AR or cutting the roots leaving about 5 mm, CR) were
treated after harvest. Then, the green onions stored at 20°C for 8 days
and 1°C for 6 weeks to investigate changes in quality. When stored at
20°C, the differences in marketability between S and FP were minimal,
while when stored at 1°C, the marketability of the FP remained higher
than that of S. The leaf color change in CR progressed faster than in the AR
treatment group, leading to faster quality deterioration. The occurrence of
weight loss, browning, and softening of stems progressed as the storage period
elapsed. However, except weight loss, they were at a level that did not affect
marketability within the marketability limit period determined by color change
and wiltig of leaves. The allicin and quercetin contents of stems increased in
the early stages when quality deteriorated after harvest but decreased as
quality deterioration became more severe.
Stochastic Modeling of Intra- and Inter-Hospital Transmission in Middle East Respiratory Syndrome Outbreak
Authors: Ko Youngsuk , Lee Jacob , Jung Eunok
Published: July 2024

Middle East Respiratory Syndrome (MERS) is an endemic disease that presents a significant global health challenge characterized by a high risk of transmission within healthcare settings. Understanding both intra- and inter-hospital spread of MERS is crucial for effective disease control and prevention. This study utilized stochastic modeling simulations to capture inherent randomness and unpredictability in disease transmission. This approach provides a comprehensive understanding of potential future MERS outbreaks under various scenarios in Korea.

Our simulation results revealed a broad distribution of case number, with a mean of 70 and a credible interval of [0, 315]. Additionally, we assessed the risks associated with delayed outbreak detection and investigated the preventive impact of mask mandates within hospitals. Our findings emphasized the critical role of early detection and the implementation of preventive measures in curbing the spread of infectious diseases. Specifically, even under the worst-case scenario of late detection, if mask mandates achieve a reduction effect exceeding 55%, the peak number of isolated cases would remain below 50.

The findings derived from this study offer valuable guidance for policy decisions and healthcare practices, ultimately contributing to the mitigation of future outbreaks. Our research underscores the critical role of mathematical modeling in comprehending and predicting disease dynamics, thereby enhancing ongoing efforts to prepare for and respond to MERS or other comparable infectious diseases.

Author summary

In our study, we used stochastic modeling simulations to understand the potential future outbreaks of Middle East Respiratory Syndrome (MERS) in Korea. Our simulations revealed a wide range of possible case numbers, emphasizing the unpredictable nature of disease transmission. We found that early detection of an outbreak and the implementation of preventive measures, such as mask mandates in hospitals, play a critical role in controlling the spread of infectious diseases. Even in the worst-case scenario of late detection, if masks are mandated and achieve a reduction effect exceeding 55%, the peak number of isolated cases would remain below 50. Our research highlights the importance of mathematical modeling in understanding and predicting disease dynamics, providing valuable insights for policy decisions and healthcare practices. This work contributes to the ongoing efforts to prepare for and respond to MERS or other similar infectious diseases.
Cost-effective DNA Storage System with DNA Movable Type
Authors: Wang Chenyang , Wei Di , Wei Zheng , Yang Dongxin , Xing Jing , Wang Yunze , Wang Xiaotong , Wang Pei , Ma Guannan , Zhang Xinru , Li Haolan , Tang Chuan , Hou Pengfei , Wang Jie , Gao Renjun , Xie Guiqiu , Li Cuidan , Ju Yingjiao , Wang Peihan , Yue Liya , Zhao Yongliang , Sheng Yongjie , Xiao Jingfa , Niu Haitao , Xu Sihong , Yang Huaiyi , Liu Di , Duan Bo , Bu Dongbo , Tan Guangming , Chen Fei
Published: July 2024

In the face of exponential data growth, DNA-based storage offers a promising solution for preserving big-data. However, most existing DNA storage methods, akin to traditional block printing, require costly chemical synthesis for each individual data file, adopting a sequential, one-time-use synthesis approach. To overcome these limitations, we introduce a novel, cost-effective "DNA-Movable-Type Storage" system, inspired by movable type printing. This system utilizes pre-fabricated DNA movable types-short, double-stranded DNA oligonucleotides encoding specific payload, address, and checksum data. These DNA-MTs are enzymatically ligated/assembled into cohesive sequences, termed "DNA movable type blocks", streamlining the assembly process with the automated BISHENG-1 DNA-MT inkjet printer. Using BISHENG-1, we successfully printed, assembled, stored and accurately retrieved 43.7 KB of data files in diverse formats (text, image, audio, and video)in vitroandin vivo, using only 350 DNA-MTs. Notably, each DNA-MT, synthesized once (2OD), can be used up to 10,000 times, reducing costs to 122 $/MB-outperforming existing DNA storage methods. This innovation circumvents the need to synthesize entire DNA sequences encoding files from scratch, offering significant cost and efficiency advantages. Furthermore, it has considerable untapped potential to advance a robust DNA storage system, better meeting the extensive data storage demands of the big-data era.
Full characterization of unresolved structural variation through long-read sequencing and optical genome mapping
Authors: De Clercq Griet , Vantomme Lies , Dewaele Barbara , Callewaert Bert , Vanakker Olivier , Janssens Sandra , Loeys Bart , Strazisar Mojca , Coster Wouter De , Vermeesch Joris Robert , Dheedene Annelies , Menten Björn
Published: July 2024

Structural variants (SVs) are important contributors to human disease. Their characterization remains however difficult due to their size and association with repetitive regions. Long-read sequencing (LRS) and optical genome mapping (OGM) can aid as their molecules span multiple kilobases and capture SVs in full. In this study, we selected six individuals who presented with unresolved SVs. We applied LRS onto all individuals and OGM to a subset of three complex cases. LRS detected and fully resolved the interrogated SV in all samples. This enabled a precise molecular diagnosis in two individuals. Overall, LRS identified 100% of the junctions at single-basepair level, providing valuable insights into their formation mechanisms without need for additional data sources. Application of OGM added straighaorward variant phasing, aiding in the unravelment of complex rearrangements. These results highlight the potential of LRS and OGM as follow-up molecular tests for complete SV characterization. We show that they can assess clinically relevant structural variation at unprecedented resolution. Additionally, they detect (complex) cryptic rearrangements missed by conventional methods. This ultimately leads to an increased diagnostic yield, emphasizing their added benefit in a diagnostic sehng. To aid their rapid adoption, we provide detailed laboratory and bioinformatics workflows in this manuscript.
Interpretable Machine Learning for Predicting Multiple Sclerosis Conversion from Clinically Isolated Syndrome
Authors: Daniel Eden Caroline , Tirunagari Santosh , Batth Karan , Windridge David , Balla Yashaswini
Published: July 2024

Background

Machine learning (ML) prediction of clinically isolated syndrome (CIS) conversion to multiple sclerosis (MS) could be used as a remote, preliminary tool by clinicians to identify high-risk patients that would benefit from early treatment.

Objective

This study evaluates ML models to predict CIS to MS conversion and identifies key predictors.

Methods

Five supervised learning techniques (Naïve Bayes, Logistic Regression, Decision Trees, Random Forests and Support Vector Machines) were applied to clinical data from 138 Lithuanian and 273 Mexican CIS patients. Seven different feature combinations were evaluated to determine the most effective models and predictors.

Results

Key predictors common to both datasets included sex, presence of oligoclonal bands in CSF, MRI spinal lesions, abnormal visual evoked potentials and brainstem auditory evoked potentials. The Lithuanian dataset confirmed predictors identified by previous clinical research, while the Mexican dataset partially validated them. The highest F1 score of 1.0 was achieved using Random Forests on all features for the Mexican dataset and Logistic Regression with SMOTE Upsampling on all features for the Lithuanian dataset.

Conclusion

Applying the identified high-performing ML models to the CIS patient datasets shows potential in assisting clinicians to identify high-risk patients.
On the Importance of Preserving Active Induced-Fit Conformations during Enzyme-Catalyzed Reactions: a Case Study of CARNMT1
Authors: Deng Hao , Rahman Adua , Qian Ping , Guo Hong
Published: July 2024

Considerable efforts have been made to understand how precise orientations of catalytic groups/substrate in enzyme-substrate complexes are generated for catalysis, leading to the proposals of lock-and-key, induced-fit and conformational selection models as well as their extensions. By contrast, little attention has been paid to the importance of preserving such active conformations during enzyme-catalyzed reactions to allow catalytic residues to exert their effects during catalysis, including transition state stabilization. Here MD and free energy simulations based on QM/MM potentials are carried out for CARNMT1, a histidine methyltransferase, to determine the importance and requirements for preservation of catalytic competent induced-fit conformations during methylation. We examine interplay of certain anchor residues that occupy similar positions before and after substrate binding (Asp316, Tyr386 and Tyr396) with the latch residue (His347) that is responsible for generating the active induced-fit conformation. For wild type, the catalytic competent orientations can be preserved well after the reaction passes TS allowing the active site residues to exert the effects. For the Tyr386Ala and Tyr396Asp mutants, the induced-fit conformation can be formed in the mutant-substrate complex but collapses in the early stage of reaction well before it can reach TS. Such pre-mature collapse of the active conformations as a result of the mutations is likely to be responsible for the significant reduction of catalytic efficiency. His347Phe also fails to preserve the active induced-fit conformation, and the active induced-fit conformation cannot be formed in the Asp316Ala-substrate complex. The results demonstrate the importance of preserving the active induced-fit conformation during enzyme-catalyzed reaction. They also show that generation of active induced-fit conformations of enzyme-substrate complexes may be a necessary but not sufficient condition for efficient catalysis. Interestingly, the catalytic efficiency seems to be correlated with the ability of the enzyme/mutant to preserve the active induced-fit conformation during catalysis.
Graph-based self-supervised learning for repeat detection in metagenomic assembly
Authors: Azizpour Ali , Balaji Advait , Treangen Todd J. , Segarra Santiago
Published: July 2024

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, in which genome dynamics such as horizontal gene transfer, gene duplication, and gene loss/gain complicate accurate genome assembly from metagenomic communities. Detecting repeats is a crucial first step in overcoming these challenges. To address this issue, we propose GraSSRep, a novel approach that leverages the assembly graph's structure through graph neural networks (GNNs) within a self-supervised learning framework to classify DNA sequences into repetitive and nonrepetitive categories. Specifically, we frame this problem as a node classification task within a metagenomic assembly graph. In a self-supervised fashion, we rely on a high-precision (but low-recall) heuristic to generate pseudolabels for a small proportion of the nodes. We then use those pseudolabels to train a GNN embedding and a random forest classifier to propagate the labels to the remaining nodes. In this way, GraSSRep combines sequencing features with predefined and learned graph features to achieve state-of-the-art performance in repeat detection. We evaluate our method using simulated and synthetic metagenomic data sets. The results on the simulated data highlight GraSSRep's robustness to repeat attributes, demonstrating its effectiveness in handling the complexity of repeated sequences. Additionally, experiments with synthetic metagenomic data sets reveal that incorporating the graph structure and the GNN enhances the detection performance. Finally, in comparative analyses, GraSSRep outperforms existing repeat detection tools with respect to precision and recall.
Photon-odderon interference in exclusive
χc
charmonium production at the Electron-Ion Collider
Authors: Benić Sanjin , Dumitru Adrian , Kaushik Abhiram , Motyka Leszek , Stebel Tomasz
Published: July 2024

Exclusive C=+1 scalar, axial-vector, and tensor quarkonium production in high-energy electron-proton scattering requires a C-odd t-channel exchange of a photon or a three-gluon ladder. We derive the expressions for the corresponding amplitudes. The relative phase of the photon vs three-gluon exchange amplitudes is determined by the sign of the light-front matrix element of the eikonal color current operator dabcJ+aJ+bJ+c at moderate x, and is not affected by small-x QCD evolution. Model calculations predict constructive interference, which is particularly strong for momentum transfer |t|∼1  GeV2 where the cross section for χcJ production exceeds that for pure photon exchange by up to a factor of 4. Exclusive χcJ electroproduction at the high luminosity Electron-Ion Collider occurs with well measurable rates and measurements of these processes should find evidence for the perturbative odderon exchange. We also compute the total electroproduction cross section as a function of energy and provide first estimates of the number of χcJ events per month at the Electron-Ion Collider design luminosity.

Published by the American Physical Society
2024
Color chiral Cherenkov radiation and energy loss in the quark-gluon plasma
Authors: Hansen Jeremy , Tuchin Kirill
Published: July 2024

We introduce and investigate the color chiral Cherenkov effect which consists in radiation of the circularly polarized gluons by a fast color charge moving with constant velocity in the presence of the chiral magnetic current. We derive the transition rates for all gluon polarizations. We compute the contribution of the color chiral Cherenkov effect to the parton energy loss in the quark-gluon plasma.

Published by the American Physical Society
2024
Saturation of exponents and the asymptotic fourth state of turbulence
Authors: Sreenivasan Katepalli R. , Yakhot Victor , Staroselsky Ilya , Chen Hudong
Published: July 2024

A recent discovery about the inertial range of homogeneous and isotropic turbulence is the saturation of the scaling exponents ζn for large n, defined via structure functions of order n as Sn(r)=〈(δru)n〉=A(n)rζn. We focus on longitudinal structure functions for δru between two positions that are r apart in the same direction as u. In a previous work [], two of the present authors developed a theory for ζn, which agrees with measurements for all n for which reliable data are available, and shows saturation for large n. Here, we derive expressions for the probability density functions of δru for four different states of turbulence, including the asymptotic fourth state defined by the saturation of exponents for large n. This saturation means that the scale separation is violated in favor of strongly coupled quasiordered flow structures, which likely take the form of long and thin (worm-like) structures of length L and thickness l=O(L/Re).

Published by the American Physical Society
2024
Weyl superconductivity and quasiperiodic Majorana arcs in quasicrystals
Authors: Hori Masahiro , Okugawa Ryo , Tanaka K. , Tohyama Takami
Published: July 2024

Weyl superconductivity is a topological phase in three-dimensional crystals in which the Weyl equation describes quasiparticle excitation near band-touching points in momentum space called Weyl nodes. For quasicrystals which lack translational symmetry, a theory of Weyl superconductivity has not been established, in spite of recent extensive studies on quasicrystalline topological phases. Here, we demonstrate the occurrence of quasicrystalline Weyl superconductivity by extending the definition of Weyl superconductivity to periodically stacked, two-dimensional superconducting quasicrystals. We identify quasicrystalline Weyl nodes—topologically protected point nodes in one-dimensional momentum space corresponding to the stacking direction—in terms of a topological invariant given by a change in the Bott index in quasicrystalline layers. We find that these Weyl nodes exist in pairs and that Majorana zero-energy modes protected by the nonzero Bott index between a pair of quasicrystalline Weyl nodes appear on surfaces. These Majorana zero modes form an infinite number of arcs in momentum space, densely and quasiperiodically distributed as a function of momentum in the direction of surfaces within each quasicrystalline layer. In Ammann-Beenker (Penrose) quasicrystals, the quasiperiodicity of Majorana arcs is governed by the silver (golden) ratio associated with the quasicrystalline structure.

Published by the American Physical Society
2024
Noise is resource-contextual in quantum communication
Authors: Nema Aditya , Maity Ananda G. , Strelchuk Sergii , Elkouss David
Published: July 2024

Estimating the information transmission capability of a quantum channel remains one of the fundamental problems in quantum information processing. In contrast to classical channels, the information-carrying capability of quantum channels is contextual. One of the most significant manifestations of this is the superadditivity of the channel capacity: the capacity of two quantum channels used together can be larger than the sum of the individual capacities. Here, we present a one-parameter family of channels for which, as the parameter increases, its one-way quantum and private capacities increase while its two-way capacities decrease. We also exhibit a one-parameter family of states with analogous behavior with respect to the one- and two-way distillable entanglement and secret key. Our constructions demonstrate that noise is context dependent in quantum communication.

Published by the American Physical Society
2024
Designing and building in a fragile context: the recovery of the primary school in Wadi Abu Hindi, Palestine
Authors: Battistella Alessio Dionigi , Montanari Riccardo
Published: July 2024

Purpose

The recent convergence between architecture and cultural anthropology has laid the foundations for a methodological approach that is attentive to both local specificities and the role of design. Starting from the analysis of the recovery of the primary school in the Bedouin camp of Wadi Abu Hindi in Palestine, the article intends to outline the role of the architect as a participating observer. It highlights how acting directly in the context of intervention guarantees a more effective response to local needs within spaces marked by strong conditions of inequality and marginality.

Design/methodology/approach

The methodology employed consists in using the ethnographic approach to collect qualitative data. The choice of this methodology stems from the intention to directly involve local actors in the design and execution phases.

Findings

The role of the architect as a participating observer within critical contexts shows how the activity of design is not simply limited to designing solutions but consists above all in the anticipation of all the critical aspects that may emerge in the practical execution of the works. The active participation and the adoption of a holistic outlook allow to find targeted solutions and ensure careful listening to the local needs.

Originality/value

The originality of this article consists in using an interdisciplinary approach between architecture and cultural anthropology, considering the architect as a participant observer.
Tracking the size of the estimation window in time-series data
Authors: Kwon Tae Yeon
Published: July 2024

Purpose

This paper introduces a novel method, Variance Rule-based Window Size Tracking (VR-WT), for deriving a sequence of estimation window sizes. This approach not only identifies structural change points but also ascertains the optimal size of the estimation window. VR-WT is designed to achieve accurate model estimation and is versatile enough to be applied across a range of models in various disciplines.

Design/methodology/approach

This paper proposes a new method named Variance Rule-based Window size Tracking (VR-WT), which derives a sequence of estimation window sizes. The concept of VR-WT is inspired by the Potential Scale Reduction Factor (PSRF), a tool used to evaluate the convergence and stationarity of MCMC.

Findings

Monte Carlo simulation study demonstrates that VR-WT accurately detects structural change points and select appropriate window sizes. The VR-WT is essential in applications where accurate estimation of model parameters and inference about their value, sign, and significance are critical. The VR-WT has also helped us understand shifts in parameter-based inference, ensuring stability across periods and highlighting how the timing and impact of market shocks vary across fields and datasets.

Originality/value

The first distinction of the VR-WT lies in its purpose and methodological differences. The VR-WT focuses on precise parameter estimation. By dynamically tracking window sizes, VR-WT selects flexible window sizes and enables the visualization of structural changes. The second distinction of VR-WT lies in its broad applicability and versatility. We conducted empirical applications across three fields of study: CAPM; interdependence analysis between global stock markets; and the study of time-dependent energy prices.