bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing Deep Learning and Computed Tomography to Determine Pulmonary Nodule Activity in Patients With Nontuberculous Mycobacterial-Lung Disease
Authors: Lancaster Andrew C. , Cardin Mitchell E. , Nguyen Jan A. , Mehta Tej I. , Oncel Dilek , Bai Harrison X. , Cohen Keira A. , Lin Cheng Ting 
Published: November 2023

Purpose:
To develop and evaluate a deep convolutional neural network (DCNN) model for the classification of acute and chronic lung nodules from nontuberculous mycobacterial-lung disease (NTM-LD) on computed tomography (CT).

Materials and Methods:
We collected a data set of 650 nodules (316 acute and 334 chronic) from the CT scans of 110 patients with NTM-LD. The data set was divided into training, validation, and test sets in a ratio of 4:1:1. Bounding boxes were used to crop the 2D CT images down to the area of interest. A DCNN model was built using 11 convolutional layers and trained on these images. The performance of the model was evaluated on the hold-out test set and compared with that of 3 radiologists who independently reviewed the images.

Results:
The DCNN model achieved an area under the receiver operating characteristic curve of 0.806 for differentiating acute and chronic NTM-LD nodules, corresponding to sensitivity, specificity, and accuracy of 76%, 68%, and 72%, respectively. The performance of the model was comparable to that of the 3 radiologists, who had area under the receiver operating characteristic curve, sensitivity, specificity, and accuracy of 0.693 to 0.771, 61% to 82%, 59% to 73%, and 60% to 73%, respectively.

Conclusions:
This study demonstrated the feasibility of using a DCNN model for the classification of the activity of NTM-LD nodules on chest CT. The model performance was comparable to that of radiologists. This approach can potentially and efficiently improve the diagnosis and management of NTM-LD.
Does artificial light at night alter moth community composition?
Authors: Grenis Kylee , Nufio César , Wimp Gina M. , Murphy Shannon M. 
Published: October 2023

Ecological studies investigating the effects of artificial light at night (ALAN) have primarily focused on single or a few species, and seldom on community-level dynamics. As ALAN is a potential cause of insect and biodiversity declines, community-level perspectives are essential. We empirically tested the hypothesis that moth species differentially respond to ALAN and that these responses can cause shifts in community composition. We sampled moths from prairie fragments in Colorado, USA. We tested whether local light sources, sky glow, site area and/or vegetation affected moth community diversity. We found that increased sky glow decreased moth abundance and species richness and shifted community composition. Increased sky glow shifted moth community composition when light and bait traps were combined; notably this result appears to be driven entirely by moths sampled at bait traps, which is an unbiased sampling technique. Our results show that ALAN has significant effects on moth communities and that local light sources have contrasting effects on moth community composition compared to sky glow. It is imperative that we better understand the contrasting effects of types of ALAN to comprehend the overall impacts of light pollution on biodiversity declines.
This article is part of the theme issue ‘Light pollution in complex ecological systems’.
The economic burden of cervical cancer on women in Uganda: a cross-sectional study
Authors: Dau Hallie , Nankya Esther , Naguti Priscilla , Basemera Miriam , Payne Beth A. , Vidler Marianne , Singer Joel , McNair Avery , AboMoslim Maryam , Smith Laurie , Orem Jackson , Nakisige Carolyn , Ogilvie Gina 
Published: October 2023

ABSTRACTPURPOSEThere is limited research on how a cervical cancer diagnosis financially impacts women and their families in Uganda, including the burden of out-of-pocket costs. This is important to understand because, in addition to being economic providers, women are primary caregivers. The objective of this analysis is to describe the economic impact of cervical cancer treatment, including how this differs by socio-economic status (SES) in Uganda.METHODSWe conducted a cross-sectional study from September 19, 2022 to January 17, 2023. Women were recruited from the Uganda Cancer Institute and Jinja Regional Referral Hospital, and were eligible for this study if they were ≥ of 18 years and being treated for cervical cancer. Participants completed a 45-minute survey which included questions about their out-of-pocket costs, unpaid labor, and changes in their family’s economic situation. A wealth index was constructed from the participants ownership of household items to determine their SES. Descriptive statistics were reported.RESULTSOf the 338 participants who completed the survey, 183 were from the lower SES. Women from the lower SES were significantly more likely to be older, have ≤ primary school education, and have a more advanced stage of cervical cancer. Both groups of women reported paying out-of-pocket for cervical cancer care (higher SES 95.5%, lower SES 92.3%). Only 15/338 participants stopped treatment because they could not afford it. Women of a lower SES were significantly more likely to report borrowing money (p-value=0.004) and selling possessions to pay for cancer care (p-value=0.006). With regards to unpaid labor, women from both groups reported a decrease in the amount of time that they spent caring for their children since their cervical cancer diagnosis.CONCLUSIONRegardless of their SES, women in Uganda incur out-of-pocket costs related to their cervical cancer treatment. However, there are inequities as women from the lower SES groups were more likely to borrow funds to afford treatment. Alternative payment models and further financial support could help alleviate the financial burden of cervical cancer of care on women and families in Uganda.
Amplitude modulation perception and cortical evoked potentials in children with listening difficulties and their typically-developing peers
Authors: Petley Lauren , Blankenship Chelsea , Hunter Lisa L. , Stewart Hannah J. , Lin Li , Moore David R. 
Published: October 2023

AbstractPurposeAmplitude modulations (AM) are important for speech intelligibility, and deficits in speech intelligibility are a leading source of impairment in childhood listening difficulties (LiD). The present study aimed to explore the relationships between AM perception and speech-in-noise (SiN) comprehension in children and to determine whether deficits in AM processing contribute to childhood LiD. Evoked responses were used to parse the neural origin of AM processing.MethodForty-one children with LiD and forty-four typically-developing children, ages 8-16 y.o., participated in the study. Behavioral AM depth thresholds were measured at 4 and 40 Hz. SiN tasks included the LiSN-S and a Coordinate Response Measure (CRM)-based task. Evoked responses were obtained during an AM Change detection task using alternations between 4 and 40 Hz, including the N1 of the acoustic change complex, auditory steady-state response (ASSR), P300, and a late positive response (LP). Maturational effects were explored via age correlations.ResultsAge correlated with 4 Hz AM thresholds, CRM Separated Talker scores, and N1 amplitude. Age-normed LiSN-S scores obtained without spatial or talker cues correlated with age-corrected 4 Hz AM thresholds and area under the LP curve. CRM Separated Talker scores correlated with AM thresholds and area under the LP curve. Most behavioral measures of AM perception correlated with the SNR and phase coherence of the 40 Hz ASSR. AM Change RT also correlated with area under the LP curve. Children with LiD exhibited deficits with respect to 4 Hz thresholds, AM Change accuracy, and area under the LP curve.ConclusionsThe observed relationships between AM perception and SiN performance extend the evidence that modulation perception is important for understanding SiN in childhood. In line with this finding, children with LiD demonstrated poorer performance on some measures of AM perception, but their evoked responses implicated a primarily cognitive deficit.
GGC expansion inZFHX3causes SCA4 and impairs autophagy
Authors: Figueroa Karla P. , Gross Caspar , Atienza Elena Buena , Paul Sharan , Gandelman Mandi , Haack Tobias , Kakar Naseebullah , Sturm Marc , Casadei Nicolas , Admard Jakob , Park Joohyun , Zühlke Christine , Hellenbroich Yorck , Pozojevic Jelena , Balachandran Saranya , Händler Kristian , Zittel Simone , Timmann Dagmar , Erdlenbruch Friedrich , Herrmann Laura , Feindt Thomas , Zenker Martin , Dufke Claudia , Hübener-Schmid Jeannette , Scoles Daniel R. , Koeppen Arnulf , Ossowski Stephan , Spielmann Malte , Riess Olaf , Pulst Stefan M. 
Published: October 2023

AbstractDespite linkage to 16q in 1996, the mutation for spinocerebellar ataxia type 4 (SCA4), a late-onset sensory and cerebellar ataxia, escaped detection for 25 years. Using long- read PacBio-HiFi and ONT-Nanopre sequencing and bioinformatic analysis, we identified expansion of a GGC DNA repeat in a >85% GC-rich region in exon 10 of theZFHX3gene coding for poly-glycine (polyG). In a total of 15 nuclear families from Utah and 9 from Europe, the repeat was expanded to >40 repeats in SCA4 patients accompanied by significant phenotypic variation independent of repeat size compared to the most common normal repeat size of 21 repeats. The RE event likely occurred in a frequent Swedish haplotype shared by cases from Utah and Germany. Six characteristic ultra-rare SNVs in the vicinity of the RE in cases from Utah and Lübeck (Germany) indicate a common founder event for some of the patients. In fibroblast and iPS cells, the GGC expansion leads to increased ZFHX3 protein levels, polyG aggregates, and abnormal autophagy, which normalized withZFHX3siRNA. Increasing autophagic flux may provide a therapeutic avenue for this novel polyG disease.
A Randomized Controlled Trial Comparing Erector Spinae Plane and Transversus Abdominis Plane Blocks for Postoperative Analgesia after Elective Caesarean Section
Authors: Eksteen Aidan , Wagner Janine , Kleyenstuber Thomas , Kamerman Peter 
Published: October 2023

AbstractBackgroundPeripheral abdominal nerve blocks contribute to multimodal postoperative analgesia that enhances early recovery after caesarean sections. The transversus abdominis plane (TAP) block is an established technique that offers somatic abdominal analgesia. The erector spinae plane (ESP) block is a novel fascial plane block that may offer additional visceral analgesic effects. This study aimed to compare the postoperative analgesic efficacy of bilateral ultrasound-guided ESP blocks to TAP blocks in women undergoing caesarean sections under spinal anaesthesia.MethodsSixty-six ASA grade 1-3 (≥18 years) patients undergoing elective caesarean section under spinal anaesthesia were randomly allocated to receive either ESP blocks at the T9 vertebral level (n=33) or TAP blocks (n=33). The primary outcome measure was 24-hour cumulative morphine consumption. The secondary outcomes included the time taken to perform blocks, numeric rating scale (NRS) pain scores at 6- and 24-hours, effect of pain on activities of daily living (ADLs) and care for the newborn, time to first analgesic request, severity of opioid-related side effects, and patient satisfaction.ResultsThere was no statistically significant difference in mean (SD) 24-hour cumulative morphine consumption between the ESP blocks and TAP blocks: 27 mg (14) vs 32 mg (15) (p=0.185). ESP blocks took longer to perform: 10.7 minutes (2.2) vs 9.0 minutes (2.5) (p<0.01). There were no significant differences in the other secondary outcomes.ConclusionESP blocks did not significantly reduce postoperative analgesic requirements compared to TAP blocks after caesarean section under spinal anaesthesia. The ESP block did not demonstrate significant additional visceral analgesic effects.Trial RegistrationSouth African National Clinical Trial Registry (DOH-27-102022-5278), Pan African Clinical Trials Registry (PACTR202301645957324)
Clinical validity and utility of circulating tumor DNA (ctDNA) testing in advanced non-small cell lung cancer (aNSCLC): a systematic literature review and meta-analysis
Authors: Chen Cheng , Douglas Michael P. , Ragavan Meera V. , Phillips Kathryn A. , Jansen Jeroen P. 
Published: October 2023

ABSTRACTPurposeCirculating tumor DNA (ctDNA) testing has become a promising tool to guide first-line (1L) targeted treatment for advanced non-small cell lung cancer (aNSCLC). This study aims to estimate the clinical validity (CV) and clinical utility (CU) of ctDNA-based next-generation sequencing (NGS) for oncogenic driver mutations to inform 1L treatment decisions in aNSCLC through a systematic literature review and meta-analysis.MethodsA systematic literature search was conducted in PubMed/MEDLINE and Embase to identify randomized control trials or observational studies reporting CV/CU on ctDNA testing in patients with aNSCLC. Meta-analyses were performed using bivariate random-effects models to estimate pooled sensitivity and specificity. Progression-free/overall survival (PFS/OS) was summarized for CU studies.ResultsEighteen studies were identified: 17 CV only, 2 CU only, and 1 both. Thirteen studies were included for the meta-analysis on multi-gene detection. The overall sensitivity and specificity for ctDNA detection of any mutation were 0.69 (95% CI, 0.63–0.74) and 0.99 (95% CI, 0.97–1.00) respectively. However, sensitivity varied greatly by driver gene, ranging from 0.29 (95% CI, 0.13–0.53) forROS1 to 0.77 (95% CI, 0.63–0.86) forKRAS. Two studies compared PFS with ctDNA versus tissue-based testing followed by 1L targeted therapy found no significant differences. One study reported OS curves on ctDNA-matched and tissue-matched therapies but no hazard ratios were provided.ConclusionctDNA testing demonstrated an overall acceptable diagnostic accuracy in aNSCLC patients, however, sensitivity varied greatly by driver mutation. Further research is needed, especially for uncommon driver mutations, to better understand the CU of ctDNA testing in guiding targeted treatments for aNSCLC.
FTLD targets brain regions expressing recently evolved genes
Authors: Pasquini Lorenzo , Pereira Felipe L. , Seddighi Sahba , Zeng Yi , Wei Yongbin , Illán-Gala Ignacio , Vatsavayai Sarat C. , Friedberg Adit , Lee Alex J. , Brown Jesse A. , Spina Salvatore , Grinberg Lea T. , Sirkis Daniel W. , Bonham Luke W. , Yokoyama Jennifer S. , Boxer Adam L. , Kramer Joel H. , Rosen Howard J. , Humphrey Jack , Gitler Aaron D. , Miller Bruce L. , Pollard Katherine S. , Ward Michael E. , Seeley William W. 
Published: October 2023

AbstractIn frontotemporal lobar degeneration (FTLD), pathological protein aggregation is associated with a decline in human-specialized social-emotional and language functions. Most disease protein aggregates contain either TDP-43 (FTLD-TDP) or tau (FTLD-tau). Here, we explored whether FTLD targets brain regions that express genes containing human accelerated regions (HARs), conserved sequences that have undergone positive selection during recent human evolution. To this end, we used structural neuroimaging from patients with FTLD and normative human regional transcriptomic data to identify genes expressed in FTLD-targeted brain regions. We then integrated primate comparative genomic data to test our hypothesis that FTLD targets brain regions expressing recently evolved genes. In addition, we asked whether genes expressed in FTLD-targeted brain regions are enriched for genes that undergo cryptic splicing when TDP-43 function is impaired. We found that FTLD-TDP and FTLD-tau subtypes target brain regions that express overlapping and distinct genes, including many linked to neuromodulatory functions. Genes whose normative brain regional expression pattern correlated with FTLD cortical atrophy were strongly associated with HARs. Atrophy-correlated genes in FTLD-TDP showed greater overlap with TDP-43 cryptic splicing genes compared with atrophy-correlated genes in FTLD-tau. Cryptic splicing genes were enriched for HAR genes, and vice versa, but this effect was due to the confounding influence of gene length. Analyses performed at the individual-patient level revealed that the expression of HAR genes and cryptically spliced genes within putative regions of disease onset differed across FTLD-TDP subtypes. Overall, our findings suggest that FTLD targets brain regions that have undergone recent evolutionary specialization and provide intriguing potential leads regarding the transcriptomic basis for selective vulnerability in distinct FTLD molecular-anatomical subtypes.
Inspiratory Muscle Strength Training to Improve Cardiometabolic Health in Patients with Type 2 Diabetes Mellitus: Protocol for the Diabetes Inspiratory Training (DIT) Clinical Trial
Authors: Reed Baylee L. , Tavoian Dallin , Bailey E. Fiona , Funk Janet L. , Coletta Dawn K. 
Published: October 2023

AbstractType 2 diabetes mellitus (T2DM) is a complex, chronic metabolic disease that carries with it a high prevalence of comorbid conditions, making T2DM one of the leading causes of death in the U.S. Traditional lifestyle interventions (e.g., diet, exercise) can counter some adverse effects of T2DM; however, participation in these activities is low with reasons ranging from physical discomfort to lack of time. Thus, there is a critical need to develop novel management strategies that effectively reduce cardiometabolic disease risk and address barriers to adherence. High-resistance inspiratory muscle strength training (IMST) is a time-efficient and simple breathing exercise that significantly reduces systolic and diastolic BP and improves vascular endothelial function in adults with above-normal blood pressure. Herein, we describe the study protocol for a randomized clinical trial to determine the effects of a 6 week IMST regimen on glycemic control and insulin sensitivity in adults with T2DM. Our primary outcome measures include fasting plasma glucose, fasting serum insulin, and insulin sensitivity utilizing homeostatic model assessment for insulin resistance (HOMA-IR). Secondary outcome measures include casual (resting) systolic BP and endothelial-dependent dilation. Further, we will collect plasma for exploratory proteomic analyses. This trial seeks to establish the cardiometabolic effects of 6 weeks of high-resistance IMST in patients with T2DM.
Wastewater detection of emerging arbovirus infections: Case study of Dengue in the United States
Authors: Wolfe Marlene K. , Paulos Abigail Harvey , Zulli Alessandro , Duong Dorothea , Shelden Bridgette , White Bradley J. , Boehm Alexandria B. 
Published: October 2023

AbstractClimate change and urbanization are increasing the distribution of insect vectors of infectious diseases. Dengue virus is an arbovirus that causes nearly 100 million symptomatic infections per year and is endemic in 124 countries, and the range of its mosquito vectors continues to increase. Surveillance of dengue virus infections is complicated by the fact that infections can be asymptomatic and symptoms may not be readily recognizable to clinicians. Here we show that wastewater monitoring can be used to detect dengue virus RNA to yield information about circulation of dengue infections in a community. We collected three samples of wastewater solids per week from three different wastewater treatment plants in Miami-Dade County, Florida where dengue infections have been locally acquired. Using molecular methods, we tested wastewater solids for RNA from the 4 dengue virus serotypes and consistently detected dengue virus 3 RNA at all three wastewater plants, and did not detect the other 3 serotypes. According to publicly available data on dengue infections, the vast majority of infections were caused by serotype 3. Wastewater detection of dengue virus RNA is possible with as few as 4.23 laboratory confirmed dengue cases per 1 million people, based on publicly available infection data.SynopsisDengue virus RNA was detected in wastewater solids in a location with local- and travel-associated dengue infections.
Visual boundary cues, alone, can anchor place and grid cells in virtual reality
Authors: Yang Xiuting , Cacucci Francesca , Burgess Neil , Wills Thomas , Chen Guifen 
Published: November 2023

SUMMARYThe hippocampal formation contains neurons responsive to an animal’s current location and orientation, which together provide the organism with a neural map of space1–3. Spatially tuned neurons rely on external landmark cues and internally generated movement information to estimate position4,5. An important class of landmark cue are the boundaries delimiting an environment, which can define place cell field position6,7and stabilise grid cell firing8. However, the precise nature of the sensory information used by the hippocampus to detect boundaries remains unknown. Here we use 2-dimensional virtual reality (VR)9to show that purely visual cues from the surrounding walls are both sufficient and necessary to stabilise place and grid cell responses. Unstable grid cells retain internally coherent, hexagonally arranged firing fields, but these fields ‘drift’ with respect to the virtual environment over periods >5 sec. Optic flow from a virtual floor does not slow drift dynamics, emphasising the importance of boundary-related visual information. Surprisingly, place fields are more stable close to boundaries even when these are invisible. Invisible boundary locations can only be inferred from the relative movements of the animal and a reward beacon, specifically, from the mismatch between observed beacon movement and that predicted from motor output. This shows that boundary information can be detected through sensorimotor feedback. We find that subsets of place cells show allocentric directional tuning towards the beacon, with strength of tuning correlating with place field stability when boundaries are removed.
Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition
Authors: Gogou Christos , Beugelink J Wouter , Frias Cátia P , Kresik Leanid , Jaroszynska Natalia , Drescher Uwe , Janssen Bert J C , Hindges Robert , Meijer Dimphna H 
Published: October 2023

AbstractNeuronal network formation is facilitated by recognition between synaptic cell adhesion molecules (CAMs) at the cell surface. Alternative splicing of CAMs provides additional specificity in forming neuronal connections. For the teneurin family of CAMs, alternative splicing of the EGF-repeats and NHL domain controls protein-protein interactions at the synapse. Here we present a 3.2 Å cryo-EM structure of the compact dimeric ectodomain of teneurin-3 harbouring both splice inserts. This dimer is stabilised by an EGF8-ABD contact between subunits. Cryo-EM reconstructions of all four splice variants, together with SAXS and negative stain EM, reveal compacted dimers for each, with variant-specific dimeric arrangements. This results in specifictrans-cellular interactions, as tested in cell clustering and stripe assays. The compact conformations provide a structural basis for teneurin homo- and heterophilic interactions. Altogether, our findings demonstrate how alternative splicing results in rearrangements of the dimeric subunits, influencing neuronal recognition and circuit wiring.