bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wafer-level testing of inverse-designed and adjoint-inspired dual layer Si-SiN vertical grating couplers
Authors: Van Vaerenbergh Thomas , Hooten Sean , Jain Mudit , Sun Peng , Wilmart Quentin , Seyedi Ashkan , Huang Zhihong , Fiorentino Marco , Beausoleil Ray 
Published: September 2022

Abstract
Recently, silicon photonics foundries started providing access to new dielectric stacks which can be utilized to reduce optical I/O losses. For example, in a hybrid c-Si/SiN platform, inverse design techniques can be used to create novel dual layer grating coupler (GC) designs which, in simulations, reach state-of-the-art performance. In this paper, we experimentally validate such designs for perfectly vertical single-polarization GCs in the O-band consisting of a single-etch c-Si layer with a patterned SiN overlay, fabricated using a

193

n
m

DUV immersion lithography process on

300

m
m

wafers. Here, we investigate designs generated by two different design paradigms: inverse design based on the adjoint method and adjoint-inspired design. Using wafer-level testing, we experimentally demonstrate a record low median insertion loss (IL) of

1.3

d
B

(with interquartile range of

∼

0.1

–

0.2

d
B

) for perfectly vertical coupling in DUV lithography compatible devices which is a

∼

0.5

d
B

improvement over previously demonstrated single-layer, single-etch c-Si

0

d
e
g

GCs.
Influence maximization under limited network information: seeding high-degree neighbors
Authors: Ou Jiamin , Buskens Vincent , van de Rijt Arnout , Panja Debabrata 
Published: September 2022

Abstract
The diffusion of information, norms, and practices across a social network can be initiated by compelling a small number of seed individuals to adopt first. Strategies proposed in previous work either assume full network information or a large degree of control over what information is collected. However, privacy settings on the Internet and high non-response in surveys often severely limit available connectivity information. Here we propose a seeding strategy for scenarios with limited network information: Only the degrees and connections of some random nodes are known. This new strategy is a modification of ‘random neighbor sampling’ (or ‘one-hop’) and seeds the highest-degree neighbors of randomly selected nodes. Simulating a fractional threshold model, we find that this new strategy excels in networks with heavy tailed degree distributions such as scale-free networks and large online social networks. It outperforms the conventional one-hop strategy even though the latter can seed 50% more nodes, and other seeding possibilities including pure high-degree seeding and clustered seeding.
Dark solitons in Bose–Einstein condensates: a dataset for many-body physics research
Authors: Fritsch Amilson R , Guo Shangjie , Koh Sophia M , Spielman I B , Zwolak Justyna P 
Published: September 2022

Abstract
We establish a dataset of over

1.6
×

10
4

experimental images of Bose–Einstein condensates containing solitonic excitations to enable machine learning (ML) for many-body physics research. About

33

% of this dataset has manually assigned and carefully curated labels. The remainder is automatically labeled using SolDet—an implementation of a physics-informed ML data analysis framework—consisting of a convolutional-neural-network-based classifier and object detector as well as a statistically motivated physics-informed classifier and a quality metric. This technical note constitutes the definitive reference of the dataset, providing an opportunity for the data science community to develop more sophisticated analysis tools, to further understand nonlinear many-body physics, and even advance cold atom experiments.
The American Judicial System: A Very Short Introduction
Authors: Zelden Charles L. 
Published: September 2022

Abstract
The book provides a very short, but complete introduction to the institutions and people, the rules and processes, that make up the American judicial system. Jargon free and aimed at a general reader, it explains the where, when, and who of American courts. It also makes clear the how and why behind the law as it affects everyday people. It is, in a word, a starting place to understanding the third branch of American government at both the state and the federal levels, a guide to those wishing to know the basics of the American judicial system, and a cogent synthesis of how the various elements that make up the law and legal institutions fit together.
Politics and policy
Authors: Zelden Charles L. 
Published: September 2022

Abstract
This chapter explores the interactions between courts and other parts of government. It emphasizes that courts do not operate in a vacuum, but inevitably interact with, and often struggle with, the other institutions that govern America—specifically the legislative and executive branches. Starting with the constitutional structures that shape these interactions, it moves on to discuss the power of judicial review as employed by the US Supreme Court as an example of this process of constitutional, legal, and practical interactions between the three branches of government—starting with issues of property rights and economic regulation before moving on to civil rights and liberties cases.
Certainty
Authors: Todes Daniel P. 
Published: September 2022

Abstract
For the young Pavlov, certainty resided in the Orthodox Christian faith, which he imbibed from his family and in religious school and seminary. As a teenager, however, he embraced the popular new creed of science, modernization, and Westernization propounded by the “people of the 1860s.” He abandoned seminary for scientific studies in St. Petersburg, where he learned from his mentor Il’ia Tsion a style of physiology that emphasized vivisection, experimentation, and quantitative precision in the search for precise, mechanistic laws of vital activity. Tsion’s career was abruptly destroyed, and Pavlov was forced to make his own way. He was defeated by better-connected candidates for positions in physiology. Always high-strung and depressive, he suffered nervous symptoms that physicians diagnosed as “hysteria.” In 1891, however, another series of unforeseeable events raised him suddenly to the directorship of Russia’s new, lavishly financed physiological laboratory at the Imperial Institute of Experimental Medicine.
Come the Bolsheviks
Authors: Todes Daniel P. 
Published: September 2022

Abstract
Pavlov’s political ideology featured patriotism and scientism (belief that science was the most important force for social progress). For him at age sixty-eight, the Bolshevik seizure of power was catastrophic. He considered emigration, but, assured of Lenin’s support for his science, decided to remain. In the 1920s, his lived comfortably, with a flourishing scientific enterprise. Protected by his special status, he was the Bolsheviks’ most vocal public critic. During the 1930s his opinion of Soviet power changed. Having earlier regarded it as a terrorist regime, he now saw it as his country’s government, with both crimes and achievements. Russia’s scientific institutions were increasing rapidly, and science enjoyed unprecedented cultural prestige. This, Pavlov believed, would make Bolshevism more realistic, humane, and democratic. Preoccupied by the Nazi threat, he ceased criticizing the government publicly. He wrote outraged letters to Communist leaders, however, and used his influence to save many from the gulag.
Space
Authors: Katz Mark 
Published: September 2022

Abstract
The technologies of music configure and reconfigure our relationship with space. Dating back centuries to the earliest examples of notation and printing, technology has made it possible for music to move across distances and cultures, and the circulation of music has allowed for the circulation of aesthetics, values, and power. But even when music stays rooted in place, it influences our sense of the spaces in which we encounter it. At the same time these spaces, whether caves, cathedrals, or concert halls, shape how we create and hear music. This chapter probes the relationship between music and space through case studies on architectural acoustics, printed notation and its use in Western imperialism, the boombox and Walkman, x-ray records in the U.S.S.R, and the circulation of music via portable drives in Cuba.
Reduced RNA adenosine-to-inosine editing in hippocampus vasculature associated with Alzheimer’s disease
Authors: Crooke Philip S , Tossberg John T , Heinrich Rachel M , Porter Krislyn P , Aune Thomas M 
Published: September 2022

Abstract
Alzheimer’s disease is the most common form of dementia and recent studies identify a type 1 interferon response in Alzheimer’s disease possibly driving neuro-inflammation and other Alzheimer’s disease pathologies. Loss of adenosine-to-inosine editing of endogenous Alu RNAs results in accumulation of Alu double-stranded RNAs, activation of double-stranded RNA sensors, and induction of interferon and nuclear factor kappa B regulated genes. Here, we investigated if changes in adenosine-to-inosine editing were associated with presence of Alzheimer’s disease in total prefrontal cortex, total hippocampus, cortex vasculature and hippocampus vasculature using available RNA sequencing files. We found similar levels of Alu RNA adenosine-to-inosine editing in cortex and cortex vasculature from individuals with Alzheimer’s disease or normal cognition at the time of death and brain donation. We found modest and substantial loss of adenosine-to-inosine editing in hippocampus and hippocampus vasculature, respectively, in Alzheimer’s disease relative to normal cognition and increased expression of interferon and nuclear factor kappa B regulated genes in hippocampus. Unedited Alu RNAs as found in Alzheimer’s disease hippocampus vasculature were potent innate immune activators while edited Alu RNAs as found in normal cognition hippocampus vasculature were weak innate immune activators. Taken together, our results support a model whereby loss of Alu RNA adenosine-to-inosine editing in hippocampus results in innate immune activation that may contribute to Alzheimer’s disease pathogenesis.
NOS1AP is a novel molecular target and critical factor in TDP-43 pathology
Authors: Cappelli Sara , Spalloni Alida , Feiguin Fabian , Visani Giulia , Šušnjar Urša , Brown Anna-Leigh ,   NYGC ALS Consortium, Phatnani Hemali , Kwan Justin , Sareen Dhruv , Broach James R , Simmons Zachary , Arcila-Londono Ximena , Lee Edward B , Van Deerlin Vivianna M , Shneider Neil A , Fraenkel Ernest , Ostrow Lyle W , Baas Frank , Zaitlen Noah , Berry James D , Malaspina Andrea , Fratta Pietro , Cox Gregory A , Thompson Leslie M , Finkbeiner Steve , Dardiotis Efthimios , Miller Timothy M , Chandran Siddharthan , Pal Suvankar , Hornstein Eran , MacGowan Daniel J , Heiman-Patterson Terry , Hammell Molly G , Patsopoulos Nikolaos. A , Butovsky Oleg , Dubnau Joshua , Nath Avindra , Bowser Robert , Harms Matt , Aronica Eleonora , Poss Mary , Phillips-Cremins Jennifer , Crary John , Atassi Nazem , Lange Dale J , Adams Darius J , Stefanis Leonidas , Gotkine Marc , Baloh Robert H , Babu Suma , Raj Towfique , Paganoni Sabrina , Shalem Ophir , Smith Colin , Zhang Bin , Harris Brent , Broce Iris , Drory Vivian , Ravits John , McMillan Corey , Menon Vilas , De Bardi Marco , Borsellino Giovanna , Secrier Maria , Phatnani Hemali , Romano Maurizio , Fratta Pietro , Longone Patrizia , Buratti Emanuele 
Published: September 2022

Abstract
Many lines of evidence have highlighted the role played by heterogeneous nuclear ribonucleoproteins in amyotrophic lateral sclerosis. In this study, we have aimed to identify transcripts co-regulated by TAR DNA-binding protein 43 kDa and highly conserved heterogeneous nuclear ribonucleoproteins which have been previously shown to regulate TAR DNA-binding protein 43 kDa toxicity (deleted in azoospermia-associated protein 1, heterogeneous nuclear ribonucleoprotein -Q, -D, -K and -U). Using the transcriptome analyses, we have uncovered that Nitric Oxide Synthase 1 Adaptor Protein mRNA is a direct TAR DNA-binding protein 43 kDa target, and in flies, its modulation alone can rescue TAR DNA-binding protein 43 kDa pathology. In primary mouse cortical neurons, we show that TAR DNA-binding protein 43 kDa mediated downregulation of Nitric Oxide Synthase 1 Adaptor Protein expression strongly affects the NMDA-receptor signalling pathway. In human patients, the downregulation of Nitric Oxide Synthase 1 Adaptor Protein mRNA strongly correlates with TAR DNA-binding protein 43 kDa proteinopathy as measured by cryptic Stathmin-2 and Unc-13 homolog A cryptic exon inclusion. Overall, our results demonstrate that Nitric Oxide Synthase 1 Adaptor Protein may represent a novel disease-relevant gene, potentially suitable for the development of new therapeutic strategies.
Co-administration of Oral Cholera Vaccine With Oral Polio Vaccine Among Bangladeshi Young Children: A Randomized Controlled Open Label Trial to Assess Interference
Authors: Islam Md Taufiqul , Date Kashmira , Khan Ashraful Islam , Bhuiyan Taufiqur Rahman , Khan Zahid Hasan , Ahmed Shamim , Hossain Motaher , Khaton Fatema , Zaman K , McMillan Nigel A J , Anand Abhijeet , An Qian , Zhang Chenhua , Weldon William C , Yu Alexander , Luby Stephen , Qadri Firdausi 
Published: September 2022

Abstract

Background
Cholera remains a public health threat for low- and middle-income countries, particularly in Asia and Africa. Shanchol™, an inactivated oral cholera vaccine (OCV) is currently in use globally. OCV and oral poliovirus vaccines (OPV) could be administered concomitantly, but the immunogenicity and safety of coadministration among children aged 1–3 years is unknown.

Methods
We undertook an open-label, randomized, controlled, inequality trial in Dhaka city, Bangladesh. Healthy children aged 1–3 years were randomly assigned to 1 of 3 groups: bivalent OPV (bOPV)-alone, OCV-alone, or combined bOPV + OCV and received vaccines on the day of enrollment and 28 days later. Blood samples were collected on the day of enrollment, day 28, and day 56. Serum poliovirus neutralizing antibodies and vibriocidal antibodies against Vibrio cholerae O1 were assessed using microneutralization assays.

Results
A total of 579 children aged 1‒3 years were recruited, 193 children per group. More than 90% of the children completed visits at day 56. Few adverse events following immunization were recorded and were equivalent among study arms. On day 28, 60% (90% confidence interval: 53%–67%) and 54% (46%–61%) of participants with co-administration of bOPV + OCV responded to polioviruses type 1 and 3, respectively, compared to 55% (47%–62%) and 46% (38%–53%) in the bOPV-only group. Additionally, &gt;50% of participants showed a ≥4-fold increase in vibriocidal antibody titer responses on day 28, comparable to the responses observed in OCV-only arm.

Conclusions
Co-administration of bOPV and OCV is safe and effective in children aged 1–3 years and can be cost-beneficial.

Clinical Trial Registration
ClinicalTrials.gov (NCT03581734).
Association of Treated and Untreated Chronic Hepatitis C With the Incidence of Active Tuberculosis Disease: A Population-Based Cohort Study
Authors: Baliashvili Davit , Blumberg Henry M , Benkeser David , Kempker Russell R , Shadaker Shaun , Averhoff Francisco , Gvinjilia Lia , Adamashvili Natalia , Magee Matthew , Kamkamidze George , Zakalashvili Mamuka , Tsertsvadze Tengiz , Sharvadze Lali , Chincharauli Mamuka , Tukvadze Nestan , Gandhi Neel R 
Published: September 2022

Abstract

Background
Hepatitis C virus (HCV) infection causes dysregulation and suppression of immune pathways involved in the control of tuberculosis (TB) infection. However, data on the role of chronic hepatitis C as a risk factor for active TB are lacking. We sought to evaluate the association between HCV infection and the development of active TB.

Methods
We conducted a cohort study in Georgia among adults tested for HCV antibodies (January 2015–September 2020) and followed longitudinally for the development of newly diagnosed active TB. Data were obtained from the Georgian national programs of hepatitis C and TB. The exposures of interest were untreated and treated HCV infection. A Cox proportional hazards model was used to calculate adjusted hazard ratios (aHRs).

Results
A total of 1 828 808 adults were included (median follow-up time: 26 months; IQR: 13–39 months). Active TB was diagnosed in 3163 (0.17%) individuals after a median of 6 months follow-up (IQR: 1–18 months). The incidence rate per 100 000 person-years was 296 among persons with untreated HCV infection, 109 among those with treated HCV infection, and 65 among HCV-negative persons. In multivariable analysis, both untreated (aHR = 2.9; 95% CI: 2.4–3.4) and treated (aHR = 1.6; 95% CI: 1.4–2.0) HCV infections were associated with a higher hazard of active TB, compared with HCV-negative persons.

Conclusions
Adults with HCV infection, particularly untreated individuals, were at higher risk of developing active TB disease. Screening for latent TB infection and active TB disease should be part of clinical evaluation of people with HCV infection, especially in high-TB-burden areas.
Treatment of Nontuberculous Mycobacterial (NTM) Pulmonary Infection in the US Bronchiectasis and NTM Registry: Treatment Patterns, Adverse Events, and Adherence to American Thoracic Society/Infectious Disease Society of America Treatment Guidelines
Authors: Ku Jennifer H , Henkle Emily , Aksamit Timothy R , Barker Alan , Brunton Amanda E , Winthrop Kevin L ,   for the Bronchiectasis and NTM Research Registry investigators
Published: September 2022

Abstract
Among 1038 participants with pulmonary Mycobacterium avium complex and 120 with Mycobacterium abscessus enrolled in the US Bronchiectasis and NTM Research Registry, less than half received antibiotic therapy in the 24 months before registry enrollment, of which less than half were guideline based. Adverse effects occurred in 21% of therapy recipients, of whom 33% discontinued therapy.
Glucose protects the cell membrane, Na+/K+-ATPase, nucleic acids, and proteins in Bacillus subtilis spores under high pressure thermal sterilization
Authors: Bi Ke , Zhang Zhong , Shang Binling , Xin Weishan , Zhang Bianfei , Yang Jie , Liu Yue 
Published: September 2022

ABSTRACT
The extreme resistance of bacterial spores to sterilization makes them a major concern to the food industry and consumers. In this study, the effect of glucose on the inactivation of Bacillus subtilis spores by high pressure thermal sterilization (HPTS) was evaluated. The results showed that the protective effects of glucose increased with the increase in its concentration. Compared with the HPTS control (no addition of glucose), the activity of Na+/K+-ATPase was increased, the leakage of proteins and the release of 2,6-pyridine dicarboxylic acid (DPA) was decreased, and the vibrational strength of the functional group P = O was reduced by the addition of glucose. At the same time, glucose treatment increased the content of α-helix by 6%–22%, while decreased the random coil content by 5%–13% of the cellular protein. In conclusion, the addition of glucose protected the cell membrane, Na+/K+-ATPase, cellular nucleic acids and proteins of B. subtilis under HPTS treatment.
Cryptococcus neoformansreleases proteins during intracellular residence that affect the outcome of the fungal–macrophage interaction
Authors: Jung Eric H , Park Yoon-Dong , Dragotakes Quigly , Ramirez Lia S , Smith Daniel Q , Reis Flavia C G , Dziedzic Amanda , Rodrigues Marcio L , Baker Rosanna P , Williamson Peter R , Jedlicka Anne , Casadevall Arturo , Coelho Carolina 
Published: September 2022

AbstractCryptococcus neoformans is a facultative intracellular pathogen that can replicate and disseminate in mammalian macrophages. In this study, we analyzed fungal proteins identified in murine macrophage-like cells after infection with C. neoformans. To accomplish this, we developed a protocol to identify proteins released from cryptococcal cells inside macrophage-like cells; we identified 127 proteins of fungal origin in infected macrophage-like cells. Among the proteins identified was urease, a known virulence factor, and others such as transaldolase and phospholipase D, which have catalytic activities that could contribute to virulence. This method provides a straightforward methodology to study host–pathogen interactions. We chose to study further Yeast Oligomycin Resistance (Yor1), a relatively uncharacterized protein belonging to the large family of ATP binding cassette transporter (ABC transporters). These transporters belong to a large and ancient protein family found in all extant phyla. While ABC transporters have an enormous diversity of functions across varied species, in pathogenic fungi they are better studied as drug efflux pumps. Analysis of C. neoformans yor1Δ strains revealed defects in nonlytic exocytosis, capsule size, and dimensions of extracellular vesicles, when compared to wild-type strains. We detected no difference in growth rates and cell body size. Our results indicate that C. neoformans releases a large suite of proteins during macrophage infection, some of which can modulate fungal virulence and are likely to affect the fungal–macrophage interaction.
Ushering in a new era of single-cell transcriptomics in bacteria
Authors: Homberger Christina , Barquist Lars , Vogel Jörg 
Published: September 2022

AbstractTranscriptome analysis of individual cells by single-cell RNA-seq (scRNA-seq) has become routine for eukaryotic tissues, even being applied to whole multicellular organisms. In contrast, developing methods to read the transcriptome of single bacterial cells has proven more challenging, despite a general perception of bacteria as much simpler than eukaryotes. Bacterial cells are harder to lyse, their RNA content is about two orders of magnitude lower than that of eukaryotic cells, and bacterial mRNAs are less stable than their eukaryotic counterparts. Most importantly, bacterial transcripts lack functional poly(A) tails, precluding simple adaptation of popular standard eukaryotic scRNA-seq protocols that come with the double advantage of specific mRNA amplification and concomitant depletion of rRNA. However, thanks to very recent breakthroughs in methodology, bacterial scRNA-seq is now feasible. This short review will discuss recently published bacterial scRNA-seq approaches (MATQ-seq, microSPLiT, and PETRI-seq) and a spatial transcriptomics approach based on multiplexed in situ hybridization (par-seqFISH). Together, these novel approaches will not only enable a new understanding of cell-to-cell variation in bacterial gene expression, they also promise a new microbiology by enabling high-resolution profiling of gene activity in complex microbial consortia such as the microbiome or pathogens as they invade, replicate, and persist in host tissue.
Harish-Chandra Pairs in the Verlinde Category in Positive Characteristic
Authors: Venkatesh Siddharth 
Published: September 2022

Abstract
In this article, we develop the theory of commutative and cocommutative Hopf algerbas in the Verlinde category and prove that the category of affine group schemes of finite type in the Verlinde category is equivalent to the category of Harish-Chandra pairs in the Verlinde category. Subsequently, we extend this equivalence to an equivalence between corresponding representation categories.