bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating the effects of race and social vulnerability on hospital admission and mortality from COVID-19
Authors: Landman Joshua M , Steger-May Karen , Joynt Maddox Karen E , Hammond Gmerice , Gupta Aditi , Rauseo Adriana M , Zhao Min , Foraker Randi E 
Published: December 2021

Abstract

Objective
To estimate the risk of hospital admission and mortality from COVID-19 to patients and measure the association of race and area-level social vulnerability with those outcomes.

Materials and Methods
Using patient records collected at a multisite hospital system from April 2020 to October 2020, the risk of hospital admission and the risk of mortality were estimated for patients who tested positive for COVID-19 and were admitted to the hospital for COVID-19, respectively, using generalized estimating equations while controlling for patient race, patient area-level social vulnerability, and time course of the pandemic.

Results
Black individuals were 3.57 as likely (95% CI, 3.18–4.00) to be hospitalized than White people, and patients living in the most disadvantaged areas were 2.61 times as likely (95% CI, 2.26–3.02) to be hospitalized than those living in the least disadvantaged areas. While Black patients had lower raw mortality than White patients, mortality was similar after controlling for comorbidities and social vulnerability.

Discussion
Our findings point to potent correlates of race and socioeconomic status, including resource distribution, employment, and shared living spaces, that may be associated with inequitable burden of disease across patients of different races.

Conclusions
Public health and policy interventions should address these social factors when responding to the next pandemic.
Mapping the Use of Open Source Research in UN Human Rights Investigations
Authors: Murray Daragh , McDermott Yvonne , Koenig K Alexa 
Published: December 2021

Abstract
Open source information, particularly digital open source information that is publicly available on the internet, plays an increasingly central role in the landscape of human rights investigations. This article provides a thorough analysis of how open source information is used in practice by UN human rights fact-finding missions, commissions of inquiry and other official human rights investigations. Combining data from semi-structured interviews carried out with investigators with specific experience in open source human rights investigations with a review of reports and other primary and secondary sources, it examines the utility of open source information to UN human rights investigative bodies. It posits that open source research can offer tremendous benefits in planning investigations, supplying lead evidence, and providing direct evidence of violations, thereby overcoming some of the access barriers that investigators face, and potentially giving voice to a wider range of perspectives. On the other hand, this article argues that open source investigations should be approached with a clear eye to their challenges and possible pitfalls. These include the gaps of open source information and the potential to silence already-marginalized communities through open source investigations, as well as the resource-intensive nature of these investigations, the danger that open source information can affect witnesses’ perceptions, and the risks posed by online disinformation. As open source research is likely to comprise an important component of the human rights investigator’s toolbox in the future, this article argues in favour of the institutional buy-in, resourcing, and methodological rigour that it deserves.
Growing judicial support for a ‘Formstein’ defence in English patent litigation
Authors: Pendock Bethany , Kakkaiyadi Krishna , Taylor Sarah 
Published: December 2021

Abstract
Facebook Ireland Limited v Voxer IP LLC [2021] EWHC 1377 (Pat), 26 May 2021
The English Patents Court has considered the effects of a Formstein defence in the context of an infringement argument based on the doctrine of equivalents and has opined that a successful Formstein defence should result in a finding of non-infringement rather than a finding that the patent is invalid.
A novel method for skin marking in radiotherapy: first clinical use of temporary organic tattoo seal
Authors: Goto Masaaki , Oshiro Yoshiko , Tamaki Yoshio , Ishida Toshiki , Kato Yuichi , Shinoda Kazuya , Sakurai Hideyuki 
Published: December 2021

Abstract
An oil-based pen is widely used as a skin marker for identification of the isocenter and computed tomography (CT)-coordinate origin during radiotherapy. However, use of this pen has some disadvantages, including color loss and color migration. To address these problems, we have developed use of a temporary fashion tattoo (Inkbox) for skin marking. The utility and feasibility of Inkbox as an alternative to an oil-based pen were evaluated in this study. The study included patients from two centers who required skin marking for radiotherapy performed between December 2020 and March 2021. Skin markings were made with an oil-based pen or with Inkbox. The durability was recorded during daily irradiation. Skin markings with Inkbox were made in 32 patients. The total number of skin markings was 94: 64 with Inkbox and 30 with an oil-based pen. A questionnaire survey to evaluate each method was conducted among patients after radiotherapy. The median durations of marking were 16 and 4 days with Inkbox and an oil-based pen, respectively (p-value &lt; 0.001). The survey showed that Inkbox had less impact on the daily lives of patients, including reduced color migration to clothes and less concern about disappearance of the marking. There were no adverse cutaneous side effects with Inkbox. The duration of marking with Inkbox is about 16 days, with little impact on daily life. These findings suggest that Inkbox is a potentially useful method of skin marking in radiotherapy.
Scarless total thyroidectomy via transoral endoscopic vestibular approach: initial case series in a developing Asian country
Authors: Yap Ralph Victor , Villamor Jr Manuel 
Published: December 2021

AbstractConventional open thyroidectomy may leave a visible scar postoperatively and can lead to impaired quality of life. Since 2016, the transoral endoscopic thyroidectomy via vestibular approach (TOETVA) has gained popularity due to being a true ‘scarless’ procedure. However, minimally invasive thyroidectomy has not been widely adopted in the Philippines yet. From August 2019 to December 2019, nine patients (mean thyroid nodule size of 3.1 cm) underwent TOETVA with one open conversion due to adherent papillary cancer. Majority had a blood loss of &lt;100 ml, whereas mean operative time was 149.8 ± 20.5 minutes. Five patients developed hypocalcemia (three transient), whereas two patients reported transient lower lip numbness. TOETVA is a safe and feasible novel procedure for both benign and malignant thyroid diseases. Care must be taken in selecting patients who opt for TOETVA, and that surgeons should reassess their limitations before implementing this technique in their surgical practice.
Appendicitis and ganglioneuroma—an unusual co-existence
Authors: Koullouros Michalis , Candler Sarah , Smith Caroline , Olakkengil Santosh 
Published: December 2021

Abstract
Ganglioneuromas are benign, fully differentiated mature tumours related to neuronal tissues and usually seen in the gastrointestinal tract, retroperitoneum and mediastinum. The few cases of appendiceal ganglioneuromas that were previously described in the literature belong to the paediatric population and were associated with genetic mutations and syndromes. We present a unique case of an Aboriginal Australian adult with acute appendicitis and concurrent ganglioneuroma diagnosed using histopathology and immunohistochemistry using Neu-N, S100 and Sox-10. The patient had no history of any of the syndromes associated with ganglioneuromatosis and had no other relevant family history.
Cytosolic fumarase acts as a metabolic fail-safe for both high and low temperature acclimation ofArabidopsis thaliana
Authors: Saunders Helena A , Calzadilla Pablo I , Schwartz Jean-Marc , Johnson Giles N 
Published: December 2021

AbstractPlants acclimate their photosynthetic capacity (Pmax) in response to changing environmental conditions. In Arabidopsis thaliana, photosynthetic acclimation to cold requires the accumulation of the organic acid fumarate, catalysed by a cytosolically localized fumarase, FUM2. However, the role of this accumulation is currently unknown. Here, we use an integrated experimental and modelling approach to examine the role of FUM2 and fumarate across the physiological temperature range. We have studied three genotypes: Col-0; a fum2 mutant in a Col-0 background; and C24, an accession with reduced FUM2 expression. While low temperature causes an increase in Pmax in the Col-0 plants, this parameter decreases following exposure of plants to 30 °C for 7 d. Plants in which fumarate accumulation is partially (C24) or completely (fum2) abolished show a reduced acclimation of Pmax across the physiological temperature range (i.e. Pmax changes less in response to changing temperature). To understand the role of fumarate accumulation, we have adapted a reliability engineering technique, Failure Mode and Effect Analysis (FMEA), to formalize a rigorous approach for ranking metabolites according to the potential risk that they pose to the metabolic system. FMEA identifies fumarate as a low-risk metabolite, while its precursor, malate, is shown to be high risk and liable to cause system instability. We propose that the role of FUM2 is to provide a fail-safe in order to control malate concentration, maintaining system stability in a changing environment. We suggest that FMEA is a technique that is not only useful in understanding plant metabolism but can also be used to study reliability in other systems and synthetic pathways.
Quantification of radiation-induced DNA double strand break repair foci to evaluate and predict biological responses to ionizing radiation
Authors: Penninckx Sébastien , Pariset Eloise , Cekanaviciute Egle , Costes Sylvain V 
Published: December 2021

Abstract
Radiation-induced foci (RIF) are nuclear puncta visualized by immunostaining of proteins that regulate DNA double-strand break (DSB) repair after exposure to ionizing radiation. RIF are a standard metric for measuring DSB formation and repair in clinical, environmental and space radiobiology. The time course and dose dependence of their formation has great potential to predict in vivo responses to ionizing radiation, predisposition to cancer and probability of adverse reactions to radiotherapy. However, increasing complexity of experimentally and therapeutically setups (charged particle, FLASH …) is associated with several confounding factors that must be taken into account when interpreting RIF values. In this review, we discuss the spatiotemporal characteristics of RIF development after irradiation, addressing the common confounding factors, including cell proliferation and foci merging. We also describe the relevant endpoints and mathematical models that enable accurate biological interpretation of RIF formation and resolution. Finally, we discuss the use of RIF as a biomarker for quantification and prediction of in vivo radiation responses, including important caveats relating to the choice of the biological endpoint and the detection method. This review intends to help scientific community design radiobiology experiments using RIF as a key metric and to provide suggestions for their biological interpretation.
Characterization of the consensus mucosal microbiome of colorectal cancer
Authors: Zhao Lan , Grimes Susan M , Greer Stephanie U , Kubit Matthew , Lee HoJoon , Nadauld Lincoln D , Ji Hanlee P 
Published: December 2021

Abstract
Dysbioisis is an imbalance of an organ's microbiome and plays a role in colorectal cancer pathogenesis. Characterizing the bacteria in the microenvironment of a cancer through genome sequencing has advantages compared to culture-based profiling. However, there are notable technical and analytical challenges in characterizing universal features of tumor microbiomes. Colorectal tumors demonstrate microbiome variation among different studies and across individual patients. To address these issues, we conducted a computational study to determine a consensus microbiome for colorectal cancer, analyzing 924 tumors from eight independent RNA-Seq data sets. A standardized meta-transcriptomic analysis pipeline was established with quality control metrics. Microbiome profiles across different cohorts were compared and recurrently altered microbial shifts specific to colorectal cancer were determined. We identified cancer-specific set of 114 microbial species associated with tumors that were found among all investigated studies. Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were among the four most abundant phyla for the colorectal cancer microbiome. Member species of Clostridia were depleted and Fusobacterium nucleatum was one of the most enriched bacterial species in tumors. Associations between the consensus species and specific immune cell types were noted. Our results are available as a web data resource for other researchers to explore (https://crc-microbiome.stanford.edu).
OLOGRAM-MODL: mining enrichedn-wise combinations of genomic features with Monte Carlo and dictionary learning
Authors: Ferré Quentin , Capponi Cécile , Puthier Denis 
Published: December 2021

AbstractMost epigenetic marks, such as Transcriptional Regulators or histone marks, are biological objects known to work together in n-wise complexes. A suitable way to infer such functional associations between them is to study the overlaps of the corresponding genomic regions. However, the problem of the statistical significance of n-wise overlaps of genomic features is seldom tackled, which prevent rigorous studies of n-wise interactions. We introduce OLOGRAM-MODL, which considers overlaps between n ≥ 2 sets of genomic regions, and computes their statistical mutual enrichment by Monte Carlo fitting of a Negative Binomial distribution, resulting in more resolutive P-values. An optional machine learning method is proposed to find complexes of interest, using a new itemset mining algorithm based on dictionary learning which is resistant to noise inherent to biological assays. The overall approach is implemented through an easy-to-use CLI interface for workflow integration, and a visual tree-based representation of the results suited for explicability. The viability of the method is experimentally studied using both artificial and biological data. This approach is accessible through the command line interface of the pygtftk toolkit, available on Bioconda and from https://github.com/dputhier/pygtftk
Therapy for Diffuse Astrocytic and Oligodendroglial Tumors in Adults: ASCO-SNO Guideline
Authors: Mohile Nimish A , Messersmith Hans , Gatson Na Tosha N , Hottinger Andreas F , Lassman Andrew B , Morton Jordan , Ney Douglas , Nghiemphu Phioanh Leia , Olar Adriana , Olson Jeffery , Perry James , Portnow Jana , Schiff David , Shannon Anne , Shih Helen A , Strowd Roy , van den Bent Martin , Ziu Mateo , Blakeley Jaishri 
Published: December 2021

Abstract

Purpose
To provide guidance to clinicians regarding therapy for diffuse astrocytic and oligodendroglial tumors in adults.

Methods
ASCO and the Society for Neuro-Oncology convened an Expert Panel and conducted a systematic review of the literature.

Results
Fifty-nine randomized trials focusing on therapeutic management were identified.

Recommendations
Adults with newly diagnosed oligodendroglioma, isocitrate dehydrogenase (IDH)–mutant, 1p19q codeleted CNS WHO grade 2 and 3 should be offered radiation therapy (RT) and procarbazine, lomustine, and vincristine (PCV). Temozolomide (TMZ) is a reasonable alternative for patients who may not tolerate PCV, but no high-level evidence supports upfront TMZ in this setting. People with newly diagnosed astrocytoma, IDH-mutant, 1p19q non-codeleted CNS WHO grade 2 should be offered RT with adjuvant chemotherapy (TMZ or PCV). People with astrocytoma, IDH-mutant, 1p19q non-codeleted CNS WHO grade 3 should be offered RT and adjuvant TMZ. People with astrocytoma, IDH-mutant, CNS WHO grade 4 may follow recommendations for either astrocytoma, IDH-mutant, 1p19q non-codeleted CNS WHO grade 3 or glioblastoma, IDH-wildtype, CNS WHO grade 4. Concurrent TMZ and RT should be offered to patients with newly diagnosed glioblastoma, IDH-wildtype, CNS WHO grade 4 followed by 6 months of adjuvant TMZ. Alternating electric field therapy, approved by the US Food and Drug Administration, should be considered for these patients. Bevacizumab is not recommended. In situations in which the benefits of 6-week RT plus TMZ may not outweigh the harms, hypofractionated RT plus TMZ is reasonable. In patients age ≥ 60 to ≥ 70 years, with poor performance status or for whom toxicity or prognosis are concerns, best supportive care alone, RT alone (for MGMTpromoter unmethylated tumors), or TMZ alone (for MGMT promoter methylated tumors) are reasonable treatment options. Additional information is available at www.asco.org/neurooncology-guidelines.
The Epistemology of Debunking Argumentation
Authors: Egeland Jonathan 
Published: December 2021

AbstractThere is an ever-growing literature on what exactly the condition or criterion is that enables some (but not all) debunking arguments to undermine our beliefs. In this paper, I develop a novel schema for debunking argumentation, arguing that debunking arguments generally have a simple and valid form, but that whether or not they are sound depends on the particular aetiological explanation which the debunker provides in order to motivate acceptance of the individual premises. The schema has three unique features: (1) it satisfies important desiderata for what any acceptable account of debunking would have to look like; (2) it is consistent with the inductively supported claim that there is no special debunking principle; and (3) it coheres with the plausible claim that what makes debunking arguments unique is that they rely on so-called genealogies for the justification of their premises.
Characterizing heat mitigation strategies utilized by beef processors in the United States
Authors: Davis Melissa K , Engle Terry E , Cadaret Caitlin N , Cramer M Caitlin , Bigler Libby J , Wagner John J , Edwards-Callaway Lily N 
Published: December 2021

Abstract
During lairage at slaughter plants, cattle can be exposed to extreme heat conditions from pen densities and holding pen microclimates. While research outlining heat mitigation strategies used in other sectors of the beef supply chain is available, there is no published data on the use of heat mitigation strategies at slaughter plants. The objective of this study was to characterize short-term heat mitigation strategies used by commercial beef slaughter plants in the United States. Twenty-one beef slaughter plants, representing an estimated 60% of beef slaughter in the United States, were included in the study. All plants indicated use of at least one heat mitigation strategy, and five of them used more than one type. Sprinklers/misters were the most commonly used heat mitigation type (n = 17, 81%), and fans were the least common type (n = 4, 19%). Shade usage was present in several plants (n = 7, 33%), ranging from barn style roofs to shade cloths. Respondents indicated that they believed heat mitigation strategies provide benefits both to cattle well-being and meat quality outcomes. Future research should focus on the effectiveness of these techniques in improving animal well-being and quality outcomes in the slaughter plant environment and protocols for optimum implementation.
Adding Insult to Injury: Levator Ani Avulsion in Women With Obstetric Anal Sphincter Injuries
Authors: Heliker Bhumy Davé , Kenton Kimberly , Leader-Cramer Alix , Brown Oluwateniola , Bochenska Katarzyna , Geynisman-Tan Julia , Mueller Margaret , Lewicky-Gaupp Christina 
Published: December 2021

(Abstracted from Female Pelvic Med Reconstr Surg 2021;27:462–467)
Obstetric anal sphincter injuries (OASIS) and levator ani avulsion (LA) are 2 of the more widely studied neuromuscular birth injuries. Although they may occur together, sometimes they do not.
Video Head Impulse Test in Darkness, Without Visual Fixation: A Study on Healthy Subjects
Authors: Pérez-Vázquez Paz , Franco-Gutiérrez Virginia 
Published: December 2021

Objective:
The head impulse test (HIT) is triggered by the vestibulo-ocular reflex (VOR), complemented by the optokinetic and pursuit systems. This study aimed to evaluate the possibility of individualizing the VOR contribution to the HIT.

Design:
Thirty-six healthy individuals (19 males, 17 females; age 21–64 years, mean 39 years) underwent horizontal video HIT (vHIT). This was first conducted in darkness, without visual fixation, and then visually tracked.

Results:
Seventy percent of the impulses delivered ocular responses opposite to the direction of the head, matching its velocity to a point where quick anticompensatory eye movements (SQEM) stopped the response (SQEM mean latency 58.21 ms, interquartile range 50–67 ms). Of these, 75% recaptured the head velocity after culmination. Thirty percent of the responses completed a bell-shaped curve. The completed bell-shaped curve gains and instantaneous gains (at 40, 60, and 80 ms) before SQEM were equivalent for both paradigms. Females completed more bell-shaped traces (42%) than males (15%); p = 0.01. The SQEM latency was longer (62.81 versus 55.71 ms, p < 0.01), and the time to recapture the bell-shaped curve was shorter (77.51 versus 92.52 ms, p < 0.01) in females than in males. The gains were comparable between sexes in both paradigms.

Conclusions:
The VOR effect can be localized in the first 70 ms of the vHIT response. In addition, other influences may take place in estimating the vHIT responses. The study of these influences might provide useful information that can be applied to patient management.
Inclusion of Older Adults Who Experience Homelessness in Laboratory-Based Audiology Research: a Feasibility Study
Authors: Shen Jing , Weller Bridget E. , Perales Jeanette Calvario 
Published: December 2021

Objectives:
The objective of this study was to recruit older adults who experience homelessness into a feasibility study on laboratory-based audiology research.

Design:
Using best practices for recruiting individuals who experience homelessness into research, we aimed to recruit 25 participants over the course of six months. The protocol included hearing health history and hearing test. Individuals were also referred to services if needed and requested.

Results:
Among the 11 study participants recruited, almost half of the individuals did not meet the inclusion criteria due to severe hearing loss, neurological disorders, and difficulty staying alert.

Conclusions:
We identified a few barriers to including older adults who experience homelessness in laboratory-based audiology research and discussed potential strategies. Our findings provide lessons for future audiology research on including a population of individuals who may be vulnerable to health disparity and often omitted from research.