bluuebunny/crossref_metadata_2025 huggingface dataset:
Mindfulness and Acceptance–Based Interventions in Physical Therapist Practice: The Time Is Now
Authors: Tatta Joe , Willgens Annette M , Palombaro Kerstin M
Published: December 2021

One in 5 adults in the United States lives with a mental illness, and many more struggle with stress-related chronic illnesses. Physical therapists often see the physical effects that stress has on the body, but there is an underutilization of evidence-based stress management strategies with patients and clients. Mindfulness and acceptance–based interventions (MABIs) constitute a family of methods that emphasize present-moment awareness, nonjudgment, and values-based living. They operate by teaching patients to cope with stressful thoughts, emotions, and physical sensations. MABIs are associated with improved health outcomes in areas commonly seen in physical therapist practice, including health promotion, physical function, injury prevention, pain management, immune function, and noncommunicable diseases. The purpose of this Perspective article is to (1) describe MABIs; (2) discuss the relevance of MABIs to physical therapist practice; (3) discuss the positive impact of MABIs for pain, sports, immune function, physical and mental health promotion, and wellness; and (4) identify MABI outcome measures related to health behavior change. It is time.

Impact

Contemporary practice requires that physical therapists manage patient care by addressing both the mind and body. Given the existing research on MABIs, it is time to translate the evidence into minimum accreditable standards for health promotion and prevention of chronic, noncommunicable disease. This approach would have far-reaching benefits for individuals, family units, communities, and society as a whole.

Lay Summary

Mindfulness instruction delivered by a physical therapist can help improve physical and mental well-being.
The Critical Role of Nutrition Care to Improve Pain Management: A Global Call to Action for Physical Therapist Practice
Authors: Tatta Joe , Nijs Jo , Elma Ömer , Malfliet Anneleen , Magnusson Dawn
Published: December 2021

Physical therapists have unique education in the comprehensive biopsychosocial assessment and treatment of chronic pain and its mechanisms. Recently, physical therapists have raised awareness regarding the impact of nutrition on promoting health and managing noncommunicable diseases. Robust evidence supports the implementation of nutrition in physical therapist education and practice. Of particular interest for the physical therapist are investigations that use dietary interventions for the treatment of chronic pain. Yet physical therapists have received little guidance regarding their role in nutrition care for pain management and may pass on opportunities to counsel their patients on the connection between nutrition and pain. Therefore, a clinical paradigm shift and unified voice within the profession is called on to encourage physical therapists to develop tailored multimodal lifestyle interventions that include nutrition care for the management of chronic pain. This Perspective describes evidence supporting the implementation of nutrition care in physical therapist practice, supports the role of nutritional pain management for physical therapists, and encourages the use of nutrition care for primary, secondary, tertiary, prevention, health promotion, and wellness related to chronic pain. To achieve these aims, this Perspective offers suggestions for how physical therapists can (1) enhance clinical decision making; (2) expand professional, jurisdictional, and personal scope of practice; (3) evolve entry-level education; and (4) stimulate new investigations in nutrition care and pain science research. In doing so, physical therapists can assert their role throughout the pain management continuum, champion innovative research initiatives, and enhance public health by reducing the impact of chronic pain.

Impact

The nutrition care process for pain management is defined as the basic duty to provide adequate and appropriate nutrition education and counseling to people living with pain. Including the nutrition care process as part of a multimodal approach to pain management provides an opportunity for physical therapists to assert their role throughout the pain management continuum. This includes championing innovative research initiatives and enhancing public health by reducing the impact of chronic pain for over 50 million Americans.
Financial Regulation in a Quantitative Model of the Modern Banking System
Authors: Begenau J , Landvoigt T
Published: December 2021

How does the shadow banking system respond to changes in capital regulation of commercial banks? We propose a quantitative general equilibrium model with regulated and unregulated banks to study the unintended consequences of regulation. Tighter capital requirements for regulated banks cause higher convenience yield on debt of all banks, leading to higher shadow bank leverage and a larger shadow banking sector. At the same time, tighter regulation eliminates the subsidies to commercial banks from deposit insurance, reducing the competitive pressures on shadow banks to take risks. The net effect is a safer financial system with more shadow banking. Calibrating the model to data on financial institutions in the US, the optimal capital requirement is around 16$\%$.
A mathematical nutrition model adequately predicts beef and dairy cow intake and biological efficiency
Authors: Lancaster Phillip A , Davis Michael E , Tedeschi Luis O , Rutledge Jack J , Cundiff Larry V
Published: December 2021

The beef cow-calf sector accounts for 70% of feed consumed and greenhouse gases emitted for the beef industry, but there is no straightforward method to measure biological efficiency in grazing conditions. The objective of this study was to evaluate a mathematical nutrition model to estimate the feed intake and biological efficiency of mature beef cows. Data from dams (N = 160) and their second and third progeny (312 pairs) were collected from 1953 through 1980. Individual feed intake was measured at 28-d intervals year-round for dams and during 240-d lactation for progeny. Body weights of progeny were measured at 28-d intervals from birth to weaning, and of dams at parturition and weaning each production cycle. The milk yield of dams was measured at 14-d intervals. Dam metabolizable energy intake (DMEI) and milk energy yield (MEL) of each cow were predicted using the Cattle Value Discovery System beef cow (CVDSbc) model for each parity. Biological efficiency (Mcal/kg) was computed as the ratio of observed or predicted DMEI to observed calf weaning weight (PWW). Pearson correlation coefficients were computed using corr.test function and model evaluation was performed using the epiR function in R software. Average (SD) dam weight, PWW, DMEI, and observed MEL were 527 (86) kg, 291 (47) kg, 9584 (2701) Mcal/production cycle, and 1029 (529) Mcal, respectively. Observed and predicted DMEI (r = 0.93 and 0.91), and observed and predicted MEL (r = 0.58 and 0.59) were positively correlated for progeny 2 and 3, respectively. The CVDSbc model under-predicted DMEI (mean bias [MB] = 1,120 ± 76 Mcal, 11.7% of observed value) and MEL (MB = 30 ± 25 Mcal, 2.9% of observed value). Observed and predicted progeny feed intake were not correlated (r = 0.01, P-value = 0.79). Observed and predicted biological efficiency were positively correlated (r = 0.80 and 0.80, P-value ≤ 0.05) for parity 2 and 3, respectively, and the CVDSbc model under-predicted biological efficiency by 11% (MB = 3.59 ± 0.25 Mcal/kg). The CVDSbc provides reasonable predictions of feed intake and biological efficiency of mature beef cows, but further refinement of the relationship between calf feed intake and milk yield is recommended to improve predictions. Mathematical nutrition models can assist in the discovery of the biological efficiency of mature beef cows.
Apical Reference Stimulation: A Possible Solution to Facial Nerve Stimulation
Authors: van der Westhuizen Jacques , Hanekom Tania , Hanekom Johan J.
Published: December 2021

Objectives:

Postimplantation facial nerve stimulation is a common side-effect of intracochlear electrical stimulation. Facial nerve stimulation occurs when electric current intended to stimulate the auditory nerve, spread beyond the cochlea to excite the nearby facial nerve, causing involuntarily facial muscle contractions. Facial nerve stimulation can often be resolved through adjustments in speech processor fitting but, in some instances, these measures exhibit limited benefit or may have a detrimental effect on speech perception. In this study, apical reference stimulation mode was investigated as a potential intervention to facial nerve stimulation. Apical reference stimulation is a bipolar stimulation strategy in which the most apical electrode is used as the reference electrode for stimulation on all the other intracochlear electrodes.

Design:

A person-specific model of the human cochlea, facial nerve and electrode array, coupled with a neural model, was used to predict excitation of auditory and facial nerve fibers. These predictions were used to evaluate the effectiveness in reducing facial nerve stimulation using apical reference stimulation. Predictions were confirmed in psychoacoustic tests by determining auditory comfort and threshold levels for the apical reference stimulation mode while capturing electromyography data in two participants.

Results:

Models predicted a favorable outcome for apical reference stimulation, as facial nerve fiber thresholds were higher and auditory thresholds were lower, in direct comparison to conventional monopolar stimulation. Psychophysical tests also illustrated decreased auditory thresholds and increased dynamic range during apical reference stimulation. Furthermore, apical reference stimulation resulted in lower electromyography energy levels, compared to conventional monopolar stimulation, which suggests a reduction in facial nerve stimulation. Subjective feedback corroborated that apical reference stimulation alleviated facial nerve stimulation.

Conclusion:

Apical reference stimulation may be a viable strategy to alleviate facial nerve stimulation considering the improvements in dynamic range and auditory thresholds, complemented with a reduction in facial nerve stimulation symptoms.
Clinical Spectrum of Positional Vertigo in an Outpatient Setting
Authors: Chen Chih-Chung , Wang Chen-Yu , Chen Po-Yueh , Chen Mei-Chien , Lee Ting-Yi , Lee Hsun-Hua
Published: December 2021

Objectives:

To explore the clinical spectrum of positional vertigo (PV) and to study the causes of PV with atypical positional nystagmus (PN) and PV without PN.

Design:

We retrospectively analyzed the registry (2425 cases) in a university hospital. Patients who actively reported PV as their main dizziness pattern were included. Candidates were divided into three groups according to their PN: (1) benign paroxysmal PV (BPPV); (2) PV with atypical PN; and (3) PV without PN. The diagnoses and reported symptoms in each group were analyzed.

Results:

PV was the most commonly (n = 518, 28.3%) reported pattern in the registry. The two most common diagnoses of PV were BPPV (n = 146, 29.2%) and vestibular migraine (VM; n = 137, 27.4%). Fifty-seven (11.4%) patients had PV with atypical PN, the majority of which was caused by VM. Moreover, 297 (59.4%) patients had PV without PN. The two main diagnoses in this group were VM and functional dizziness, although the cause remained uncertain in 23.9% of the cases of PV without PN. The odds ratio of VM was 3.95 in patients with PV who reported headaches.

Conclusions:

PV is the most common self-reported dizziness pattern and is predominantly caused by BPPV and VM. VM is the most common cause of PV with atypical PN and PV without PN. Clinicians often erroneously assume the presence of PN in those with PV. Managing PV without PN can be challenging because of the uncertainty surrounding this phenomenon. Structured patient-oriented questionnaires assist clinicians in making timely diagnoses and adjusting treatment goals accordingly.
Phonological Priming as a Lens for Phonological Organization in Children With Cochlear Implants
Authors: Lund Emily
Published: December 2021

Objectives:

To evaluate the subconscious knowledge of between-word phonological similarities in children with cochlear implants as compared with children with typical hearing.

Design:

Participants included 30 children with cochlear implants between the ages of five and seven who used primarily spoken English to communicate, 30 children matched for chronological age, and 30 children matched for vocabulary size. Participants completed an animacy judgment task in either a (a) neutral condition, (b) a phonological prime condition where the consonant and vowel onset of the pictured word was presented prior to the visual target’s appearance, (c) an inhibition prime condition where a consonant and vowel onset not matching the pictured word was presented prior to the target’s appearance. Reaction times were recorded.

Results:

Children with cochlear implants reacted differently and more slowly than children with typical hearing in both groups to the primes: children with typical hearing experienced a phonological facilitation effect in the phonological prime condition, whereas children with cochlear implants did not. Children with cochlear implants also had reaction times that, overall, were slower than children matched for chronological age but similar to children matched for vocabulary size.

Conclusions:

The different experience of children with cochlear implants with phonological facilitation and inhibition effects may indicate children with cochlear implants have phonological organization strategies that are different from those of children with typical hearing.
Aesthetic and Functional Abdominoplasty: Anatomical and Clinical Classification based on a 12-year Retrospective Study
Authors: Klinger Marco , Klinger Francesco , Giannasi Silvia , Bandi Valeria , Vinci Valeriano , Catania Barbara , Lisa Andrea , Veronesi Alessandra , Battistini Andrea , Giaccone Micol , Caviggioli Fabio , Maione Luca
Published: December 2021

Background:

Abdomen reshaping is a common plastic surgery procedure, and numerous surgical techniques have been described in the scientific literature. To standardize surgical approach, we propose our protocol that correlates patients’ anatomy with the type of procedure performed.

Methods:

Between 2008 and 2020, we retrospectively analyzed 582 consecutive female patients who underwent abdomen reshaping procedures, assessing anatomical features, complication rate, patient satisfaction, and surgical result, comparing them with previous reports in the literature. Aesthetic outcomes were evaluated with VAS scale (0–10).

Results:

Among the 582 patients recruited in the study, we performed 74 liposuctions as a single procedure, 62 mini-abdominoplasties, 28 T-inverted abdominoplasties, and 418 full-abdominoplasties. Aesthetic outcome evaluation reported a mean value of 8.2 from patients and 7.8 from surgeons. We experienced four early postoperative bleedings requiring hemostasis revision, 18 wound dehiscences, five seromas, and 24 re-interventions for aesthetic issues. We found no differences in the complication rate while comparing our data with previous reports in the literature.

Conclusions:

Our protocol and surgical technique have proved to be effective, safe, and reproducible, with high patient and surgeon satisfaction, low complication rate, and fast recovery time.
Repeatability of Corneal Deformation Response Parameters by Dynamic Ultra High-speed Scheimpflug Imaging in Normal and Keratoconus Eyes
Authors: Henriquez Maria A. , Gomez Isabel , Camino-Quezada Maythe , Izquierdo Luis , Chauca José , Binder Perry S.
Published: December 2021

Purpose:

To assess the repeatability of corneal dynamic response (CDR) parameters in normal and keratoconus (KC) eyes using ultra high-speed Scheimpflug imaging.

Methods:

Prospective, comparative, observational study, including eyes of 112 patients that underwent high-speed Scheimpflug imaging analysis (Corvis ST, OCULUS). Twenty-one CDR parameters were evaluated to asses repeatability using: coefficient of repeatability (CR), coefficient of variation, intraclass correlation coefficient (ICC) and within-subject SD. Three consecutive measurements by the same operator were performed for each eye.

Results:

There were no significant differences between the three consecutive measurements for all parameters in both normal and KC eyes. 71.42% (15 of the 21 parameters evaluated) and 85.71% (18 of the 21 parameters) were highly repeatable in the normal and KC group, respectively. The tomographic biomechanical index (TBI), corneal biomechanical index (CBI), and stiffness parameter (SPA1) showed an ICC of 0.978, 0.954, and 0.958 in normal and 0.982, 0.892, and 0.978 in KC eyes, respectively. The CR in normal eyes for TBI, CBI, and SPA1 were 0.169, 0.242, and 14.12, respectively, and for KC eyes 0.06, 0.23, and 13.64, respectively.

Conclusions:

Most of the corneal dynamic response parameters were highly repeatable in normal and KC eyes.
The SWIFT Model for Lichen Sclerosus Among Premenarchal Girls
Authors: Wang Melinda , Wininger Michael , Vash-Margita Alla
Published: December 2021

Objective/Purpose

Delay in diagnosis of childhood lichen sclerosus (LS) can be ameliorated with an efficient evaluation tool. We sought to create a useful prognostic tool for rapid and accurate risk stratification for LS in premenarchal girls.

Method

We conducted a retrospective chart review at a single institution of premenarchal girls presenting with vulvovaginal complaints at a specialty pediatric and adolescent gynecology clinic at a major academic center. Sixty-nine patients seen between July 2019 and September 2020 were used as a pilot study to create a model for LS based on 18 signs and symptoms. Accuracy of the pilot model was confirmed in a larger data set (additional 105 patients, seen between January 2017 and December 2020), and model parameters were refined through cluster-based analytics.

Results

Pilot study yielded 5 predictors for LS: soreness (S), whitening (W), urinary incontinence (I), fissures (F), and thickening of the clitoral hood (T)—SWIFT. The final refined model is given as log odds (LS) = −7 + 3·S + 17·W + 3·I + 3·F + 18·T. This model yielded a >97% accuracy in predicting LS among 174 unique patients (LS prevalence = 18%).

Conclusions

The SWIFT model accurately predicts clinical diagnosis of LS in premenarchal girls. Replication in other patient populations is highly encouraged. Awareness of LS is paramount, and an efficient, accurate evaluation tool will prove invaluable in assuring timely diagnosis and treatment for premenarchal patients.
Does Social and Religious Background Matter? A Study of the Psychosocial Impact of Human Papillomavirus on Lebanese Women
Authors: Atallah David , El Feghaly Charbel , El Feghaly Murielle , Arab Wissam , Khaddage Abir , Akiki Mira , El Kassis Nadine , Chakra Rim Abou , Chahine Georges , Moubarak Malak
Published: December 2021

Objective

The human papillomavirus (HPV) has been associated with an important psychosocial impact. This impact has been poorly evaluated in developing countries, mostly because of the lack of instruments to quantify it. The HIP questionnaire aims to measure HPV-associated affective burden. Our team has previously translated this questionnaire to Arabic and used it to assess the impact of HPV on Lebanese women.

Materials and Methods

While the HIP is a specific tool to evaluate the emotional impact of HPV, the Hospital Anxiety and Depression Scale questionnaire consists of 2 scales, anxiety and depression, and assess the psychological distress in nonpsychiatric patients. The HPV impact profile and Hospital Anxiety and Depression Scale questionnaires were administered to 118 Lebanese women with an HPV-related presentation, aiming to determine which aspect of these women's lives was mostly affected. The association with different sociodemographic factors was also assessed.

Results

Feelings of “concerns and worries” were mostly strongly felt in our population except for women with genital warts who were more concerned with the risk of transmission and the impact on their partners. All women had predominant feelings of anxiety.

Religion was a statistically significant influencing factor and employment a protective factor. Muslim women demonstrated significant adverse affects on HPV impact profile domains that included: “sexual impact,” “self-image,” “interaction with doctors,” and “health control/life impact.”

Conclusions

Different women perceive the diagnosis of HPV and HPV-related lesions differently. In this study, employment was found to play a protective role, but the biggest influencers were social and religious beliefs.
The Vaginal Microbiome: I. Research Development, Lexicon, Defining “Normal” and the Dynamics Throughout Women's Lives
Authors: Verstraelen Hans , Vieira-Baptista Pedro , De Seta Francesco , Ventolini Gary , Lonnee-Hoffmann Risa , Lev-Sagie Ahinoam
Published: December 2021

Objective

This series of articles, titled The Vaginal Microbiome, written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the current findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders.

Materials and Methods

A database search of PubMed was performed, using the search terms “vaginal microbiome” (VMB) with “research,” “normal,” “neonate,” “puberty,” “adolescent,” “menopause,” and “ethnicities,” as well as “human microbiome project.” Full article texts were reviewed. Reference lists were screened for additional articles.

Results

In the last 2 decades, many studies applying molecular techniques were performed, intending to characterize the vaginal microbiota. These studies advanced our understanding of how vaginal health is defined. The first article in this series focuses on the advancement of VMB research, technical definitions, the definition of “normal” VMB, and the dynamics of VMB throughout women's lives.

Conclusions

Understanding how microorganisms inhabiting the vagina interact with each other and with the host is important for a more complete understanding of vaginal health. The clinical application of microbial community sequencing is in its beginning, and its interpretation regarding practical clinical aspects is yet to be determined.
The Vaginal Microbiome: II. Vaginal Dysbiotic Conditions
Authors: Lev-Sagie Ahinoam , De Seta Francesco , Verstraelen Hans , Ventolini Gary , Lonnee-Hoffmann Risa , Vieira-Baptista Pedro
Published: December 2021

Objective

This series of articles, titled The Vaginal Microbiome (VMB), written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the recent findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders.

Materials and Methods

A search of PubMed database was performed, using the search terms “vaginal microbiome” with “dysbiosis,” “bacterial vaginosis,” “cytolytic vaginosis,” “desquamative inflammatory vaginitis,” and “aerobic vaginitis.” Full article texts were reviewed. Reference lists were screened for additional articles.

Results

The second article in this series focuses on vaginal dysbiotic conditions. Dysbiosis is a term describing imbalances in bacterial communities. Given that lactobacillus-dominated microbiota are thought to be the most optimal, vaginal dysbiosis is usually considered as lactobacilli-depleted VMB. Bacterial vaginosis (BV), the most common vaginal dysbiotic condition, is a polymicrobial disorder, considered the leading cause for vaginal discharge in women worldwide. In addition, we review the VMB in other vaginal conditions associated with lactobacilli depletion: desquamative inflammatory vaginitis and aerobic vaginitis. We also discuss the controversial diagnosis of cytolytic vaginosis, related with lactobacilli overgrowth.

Conclusions

Bacterial vaginosis displays complex microbiology. The heterogeneity and diversity within the genus Gardnerella may impact the progression of BV. Bacterial biofilms may contribute to the etiology and persistence of BV, and various bacteria may affect its clinical presentation and pathogenicity. Lack of lactobacilli is not always accompanied by an overgrowth of anaerobes.
The Vaginal Microbiome: III. The Vaginal Microbiome in Various Urogenital Disorders
Authors: De Seta Francesco , Lonnee-Hoffmann Risa , Campisciano Giuseppina , Comar Manola , Verstraelen Hans , Vieira-Baptista Pedro , Ventolini Gary , Lev-Sagie Ahinoam
Published: December 2021

Objective

This series of articles, titled The Vaginal Microbiome (VMB), written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the recent findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders.

Materials and Methods

A search of PubMed database was performed, using the search terms “vaginal microbiome” with “Candida,” “vaginitis,” “urinary microbiome,” “recurrent urinary tract infections,” “sexually transmitted infections,” “human immunodeficiency virus,” “human papillomavirus,” “nonspecific vaginitis,” “vulvodynia,” and “vulvovaginal symptoms.” Full article texts were reviewed. Reference lists were screened for additional articles. The third article in this series describes VMB in various urogenital disorders.

Results

Variable patterns of the VMB are found in patients with vulvovaginal candidiasis, challenging the idea of a protective role of lactobacilli. Highly similar strains of health-associated commensal bacteria are shared in both the bladder and vagina of the same individual and may provide protection against urinary tract infections. Dysbiotic VMB increases the risk of urinary tract infection. Loss of vaginal lactic acid–producing bacteria combined with elevated pH, increase the risk for sexually transmitted infections, although the exact protective mechanisms of the VMB against sexually transmitted infections are still unknown.

Conclusions

The VMB may constitute a biological barrier to pathogenic microorganisms. When the predominance of lactobacilli community is disrupted, there is an increased risk for the acquisition of various vaginal pathogents. Longitudinal studies are needed to describe the association between the host, bacterial, and fungal components of the VMB.
The Vaginal Microbiome: IV. The Role of Vaginal Microbiome in Reproduction and in Gynecologic Cancers
Authors: Ventolini Gary , Vieira-Baptista Pedro , De Seta Francesco , Verstraelen Hans , Lonnee-Hoffmann Risa , Lev-Sagie Ahinoam
Published: December 2021

Objective

This series of articles, titled The Vaginal Microbiome (VMB), written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the recent findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders.

Materials and Methods

A search of PubMed database was performed, using the search terms “vaginal microbiome” with “reproduction,” “infertility,” “fertility,” “miscarriages,” “pregnancy” “cervical cancer,” “endometrial cancer,” and “ovarian cancer.” Full article texts were reviewed. Reference lists were screened for additional articles.

Results

The fourth article of this series focuses on 2 distinct areas: the role of VMB in various aspects of human reproduction and, in sharp contrast, the association between the VMB and gynecologic malignancies. Several of the negative pregnancy outcomes have been associated with an altered VMB. Dysbiosis is remarkably linked with poor pregnancy outcomes from preconception to delivery. The associations between the microbiome and gynecologic cancers are described.

Conclusions

The development of the microbiome research, enabled by molecular-based techniques, has dramatically increased the detection of microorganisms and the understanding of bacterial communities that are relevant to maternal-fetal medicine in health and disease, as well as in gynecological malignancies. Proving causation in cancer is difficult because of the complex interactive nature of potential causative factors. Certain elements of the microbiota have been shown to provoke inflammatory reactions, whereas others produce anti-inflammatory reactions; this balance might be impaired with a change in microbial variety.
Quantum information approach to high energy interactions
Authors: Kharzeev Dmitri E.
Published: December 2021

High energy hadron interactions are commonly described by using a probabilistic parton model that ignores quantum entanglement present in the light-cone wave functions. Here, we argue that since a high energy interaction samples an instant snapshot of the hadron wave function, the phases of different Fock state wave functions cannot be measured—therefore the light-cone density matrix has to be traced over these unobservable phases. Performing this trace with the corresponding

U
(
1
)

Haar integration measure leads to ‘Haar scrambling’ of the density matrix, and to the emergence of entanglement entropy. This entanglement entropy is determined by the Fock state probability distribution, and is thus directly related to the parton structure functions. As proposed earlier, at large rapidity

η

the hadron state becomes maximally entangled, and the entanglement entropy is

S
E

∼
η

according to QCD evolution equations. When the phases of Fock state components are controlled, for example in spin asymmetry measurements, the Haar average cannot be performed, and the probabilistic parton description breaks down.

This article is part of the theme issue ‘Quantum technologies in particle physics’.
Quantum fermions from classical bits
Authors: Wetterich Christof
Published: December 2021

A simple probabilistic cellular automaton is shown to be equivalent to a relativistic fermionic quantum field theory with interactions. Occupation numbers for fermions are classical bits or Ising spins. The automaton acts deterministically on bit configurations. The genuinely probabilistic character of quantum physics is realized by probabilistic initial conditions. In turn, the probabilistic automaton is equivalent to the classical statistical system of a generalized Ising model. For a description of the probabilistic information at any given time quantum concepts as wave functions and non-commuting operators for observables emerge naturally. Quantum mechanics can be understood as a particular case of classical statistics. This offers prospects to realize aspects of quantum computing in the form of probabilistic classical computing.

This article is part of the theme issue ‘Quantum technologies in particle physics’.
From quantum link models to D-theory: a resource efficient framework for the quantum simulation and computation of gauge theories
Authors: Wiese Uwe-Jens
Published: December 2021

Quantum link models provide an extension of Wilson’s lattice gauge theory in which the link Hilbert space is finite-dimensional and corresponds to a representation of an embedding algebra. In contrast to Wilson’s parallel transporters, quantum links are intrinsically quantum degrees of freedom. In D-theory, these discrete variables undergo dimensional reduction, thus giving rise to asymptotically free theories. In this way(1+1)-dCP(N−1)models emerge by dimensional reduction from(2+1)-dSU(N)quantum spin ladders, the(2+1)-dconfiningU(1)gauge theory emerges from the Abelian Coulomb phase of a(3+1)-dquantum link model, and(3+1)-dQCD arises from a non-Abelian Coulomb phase of a(4+1)-dSU(3)quantum link model, with chiral quarks arising naturally as domain wall fermions. Thanks to their finite-dimensional Hilbert space and their economical mechanism of reaching the continuum limit by dimensional reduction, quantum link models provide a resource efficient framework for the quantum simulation and computation of gauge theories.

This article is part of the theme issue ‘Quantum technologies in particle physics’.
SARS-COV-2 Omicron variant predicted to exhibit higher affinity to ACE-2 receptor and lower affinity to a large range of neutralizing antibodies, using a rapid computational platform
Authors: Zemla Adam , Desautels Thomas , Lau Edmond Y. , Zhu Fangqiang , Arrildt Kathryn T. , Segelke Brent W. , Sundaram Shankar , Faissol Daniel
Published: December 2021

Rapid assessment of whether a pandemic pathogen may have increased transmissibility or be capable of evading existing vaccines and therapeutics is critical to mounting an effective public health response. Over the period of seven days, we utilized rapid computational prediction methods to evaluate potential public health implications of the emerging SARS-CoV-2 Omicron variant. Specifically, we modeled the structure of the Omicron variant, examined its interface with human angiotensin converting enzyme 2 (ACE-2) and evaluated the change in binding affinity between Omicron, ACE-2 and publicly known neutralizing antibodies. We also compared the Omicron variant to known Variants of Concern (VoC). Seven of the 15 Omicron mutations occurring in the spike protein receptor binding domain (RBD) occur at the ACE-2 cell receptor interface, and therefore may play a critical role in enhancing binding to ACE-2. Our estimates of Omicron RBD-ACE-2 binding affinities indicate that at least two of RBD mutations, Q493R and N501Y, contribute to enhanced ACE-2 binding, nearly doubling delta-delta-G (ddG) free energies calculated for other VoC’s. Binding affinity estimates also were calculated for 55 known neutralizing SARS-CoV-2 antibodies. Analysis of the results showed that Omicron substantially degrades binding for more than half of these neutralizing SARS-CoV-2 antibodies, and for roughly 10 times as many of the antibodies than the currently dominant Delta variant. This early study lends support to use of rapid computational risk assessments to inform public health decision-making while awaiting detailed experimental characterization and confirmation.
Neutralization and Stability of SARS-CoV-2 Omicron Variant
Authors: Zeng Cong , Evans John P. , Qu Panke , Faraone Julia , Zheng Yi-Min , Carlin Claire , Bednash Joseph S. , Zhou Tongqing , Lozanski Gerard , Mallampalli Rama , Saif Linda J. , Oltz Eugene M. , Mohler Peter , Xu Kai , Gumina Richard J. , Liu Shan-Lu
Published: December 2021

The SARS-CoV-2 B.1.1.529/Omicron variant was first characterized in South Africa and was swiftly designated a variant of concern1. Of great concern is its high number of mutations, including 30-40 mutations in the virus spike (S) protein compared to 7-10 for other variants. Some of these mutations have been shown to enhance escape from vaccine-induced immunity, while others remain uncharacterized. Additionally, reports of increasing frequencies of the Omicron variant may indicate a higher rate of transmission compared to other variants. However, the transmissibility of Omicron and its degree of resistance to vaccine-induced immunity remain unclear. Here we show that Omicron exhibits significant immune evasion compared to other variants, but antibody neutralization is largely restored by mRNA vaccine booster doses. Additionally, the Omicron spike exhibits reduced receptor binding, cell-cell fusion, S1 subunit shedding, but increased cell-to-cell transmission, and homology modeling indicates a more stable closed S structure. These findings suggest dual immune evasion strategies for Omicron, due to altered epitopes and reduced exposure of the S receptor binding domain, coupled with enhanced transmissibility due to enhanced S protein stability. These results highlight the importance of booster vaccine doses for maintaining protection against the Omicron variant, and provide mechanistic insight into the altered functionality of the Omicron spike protein.
In vitro and computational analysis of the putative furin cleavage site (RRARS) in the divergent spike protein of the rodent coronavirus AcCoV-JC34 (sub-genus luchacovirus)
Authors: Choi Annette , Singleton Deanndria T. , Stout Alison E. , Millet Jean K. , Whittaker Gary R.
Published: December 2021

The Coronaviridae is a highly diverse virus family, with reservoir hosts in a variety of wildlife species that encompass bats, birds and small mammals, including rodents. Within the taxonomic group alphacoronavirus, certain sub-genera (including the luchacoviruses) have phylogenetically distinct spike proteins, which remain essentially uncharacterized. Using in vitro and computational techniques, we analyzed the spike protein of the rodent coronavirus AcCoV-JC34 from the sub-genus luchacovirus, previously identified in Apodemus chevrieri (Chevrier’s field mouse). We show that AcCoV-JC34—unlike the other luchacoviruses—has a putative furin cleavage site (FCS) within its spike S1 domain, close to the S1/S2 interface. The pattern of basic amino acids within the AcCoV-JC34 FCS (-RR-R-) is identical to that found in “pre-variant” SARS-CoV-2—which is in itself atypical for an FCS, and suboptimal for furin cleavage. Our analysis shows that, while containing an -RR-R-motif, the AcCoV-JC34 spike “FCS” is not cleaved by furin (unlike for SARS-CoV-2), suggesting the possible presence of a progenitor sequence for viral emergence from a distinct wildlife host.
A Model Visualization-based Approach for Insight into Waveforms and Spectra Learned by CNNs
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D.
Published: December 2021

Recent years have shown a growth in the application of deep learning architectures such as convolutional neural networks (CNNs), to electrophysiology analysis. However, using neural networks with raw time-series data makes explainability a significant challenge. Multiple explainability approaches have been developed for insight into the spectral features learned by CNNs from EEG. However, across electrophysiology modalities, and even within EEG, there are many unique waveforms of clinical relevance. Existing methods that provide insight into waveforms learned by CNNs are of questionable utility. In this study, we present a novel model visualization-based approach that analyzes the filters in the first convolutional layer of the network. To our knowledge, this is the first method focused on extracting explainable information from EEG waveforms learned by CNNs while also providing insight into the learned spectral features. We demonstrate the viability of our approach within the context of automated sleep stage classification, a well-characterized domain that can help validate our approach. We identify 3 subgroups of filters with distinct spectral properties, determine the relative importance of each group of filters, and identify several unique waveforms learned by the classifier that were vital to the classifier performance. Our approach represents a significant step forward in explainability for electrophysiology classifiers, which we also hope will be useful for providing insights in future studies.

Clinical Relevance

Our approach can assist with the development and validation of clinical time-series classifiers.
Genotype and Th2 cells control monocyte to tissue resident macrophage differentiation during nematode infection of the pleural cavity
Authors: Finlay Conor M , Parkinson James E , Chan Brian HK , Ajendra Jesuthas , Chenery Alistair , Morrison Anya , Houlder Emma L , Baker Syed Murtuza , Dickie Ben , Boon Louis , MacDonald Andrew S , Konkel Joanne E , Rückerl Dominik , Allen Judith E
Published: December 2021

The recent revolution in tissue-resident macrophage biology has resulted largely from murine studies performed in the C57BL/6 strain. Here, we provide a comprehensive analysis of immune cells in the pleural cavity using both C57BL/6 and BALB/c mice. Unlike C57BL/6 mice, naïve tissue-resident Large Cavity Macrophages (LCM) of BALB/c mice failed to fully implement the tissue residency program. Following infection with a pleural-dwelling nematode these pre-existing differences were accentuated with LCM expansion occurring in C57BL/6 but not BALB/c mice. While infection drove monocyte recruitment in both strains, only in C57BL/6 mice were monocytes able to efficiently integrate into the resident pool. Monocyte to macrophage conversion required both T cells and IL-4Rα signalling. Host genetics are therefore a key influence on tissue resident macrophage biology, and during nematode infection Th2 cells control the differentiation pathway of tissue resident macrophages.

Graphical Abstract
Optimal operation of parallel mini-bioreactors in bioprocess development using multi-stage MPC
Authors: Krausch Niels , Kim Jong Woo , Lucia Sergio , Groß Sebastian , Barz Tilman , Neubauer Peter , Cruz Bournazou Mariano N.
Published: December 2021

Bioprocess development is commonly characterized by long development times, especially in the early screening phase. After promising candidates have been pre-selected in screening campaigns, an optimal operating strategy has to be found and verified under conditions similar to production. Cultivating cells with pulse-based feeding and thus exposing them to oscillating feast and famine phases has shown to be a powerful approach to study microorganisms closer to industrial bioreactor conditions. In view of the large number of strains and the process conditions to be tested, high-throughput cultivation systems provide an essential tool to sample the large design space in short time. We have recently presented a comprehensive platform, consisting of two liquid handling stations coupled with a model-based experimental design and operation framework to increase the efficiency in High Throughput bioprocess development. Using calibrated macro-kinetic growth models, the platform has been successfully used for the development of scale-down fed-batch cultivations in parallel mini-bioreactor systems. However, it has also been shown that parametric uncertainties in the models can significantly affect the prediction accuracy and thus the reliability of optimized cultivation strategies. To tackle this issue, we implemented a multi-stage Model Predictive Control (MPC) strategy to fulfill the experimental objectives under tight constraints despite the uncertainty in the parameters and the measurements. Dealing with uncertainties in the parameters is of major importance, since constraint violation would easily occur otherwise, which in turn could have adverse effects on the quality of the heterologous protein produced. Multi-stage approaches build up scenario tree, based on the uncertainty that can be encountered and computing optimal inputs that satisfy the constrains despite of such uncertainties. Using the feedback information gained through the evolution along the tree, the control approach is significantly more robust than standard MPC approaches without being overly conservative. We show in this study that the application of multi-stage MPC can increase the number of successful experiments, by applying this methodology to a mini-bioreactor cultivation operated in parallel.
Insights from the IronTract challenge: optimal methods for mapping brain pathways from multi-shell diffusion MRI
Authors: Maffei Chiara , Girard Gabriel , Schilling Kurt G. , Aydogan Dogu Baran , Adluru Nagesh , Zhylka Andrey , Wu Ye , Mancini Matteo , Hamamci Andac , Sarica Alessia , Teillac Achille , Baete Steven H. , Karimi Davood , Yeh Fang-Cheng , Yildiz Mert E. , Gholipour Ali , Bihan-Poudec Yann , Hiba Bassem , Quattrone Andrea , Quattrone Aldo , Boshkovski Tommy , Stikov Nikola , Yap Pew-Thian , de Luca Alberto , Pluim Josien , Leemans Alexander , Prabhakaran Vivek , Bendlin Barbara B. , Alexander Andrew L. , Landman Bennett A. , Canales-Rodríguez Erick J. , Barakovic Muhamed , Rafael-Patino Jonathan , Yu Thomas , Rensonnet Gaëtan , Schiavi Simona , Daducci Alessandro , Pizzolato Marco , Fischi-Gomez Elda , Thiran Jean-Philippe , Dai George , Grisot Giorgia , Lazovski Nikola , Puch Santi , Ramos Marc , Rodrigues Paulo , Prchkovska Vesna , Jones Robert , Lehman Julia , Haber Suzanne N. , Yendiki Anastasia
Published: December 2021

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.
DOK1 and DOK2 regulate CD8+ T cell signaling and memory formation without affecting tumor cell killing
Authors: Laletin V. , Bernard P.-L. , Montersino C. , Yamanashi Y. , Olive D. , Castellano R. , Guittard G. , Nunès J. A.
Published: December 2021

Targeting intracellular inhibiting proteins is a promising strategy to improve CD8+ T cell anti-tumor efficacy. DOK1 and DOK2 are CD8+ T cell inhibitory proteins that are targeted in this study in order to improve the activation and cytotoxic capacities of these cells. To evaluate the role of DOK-1 and DOK-2 depletion in physiology and effector function of T CD8+ lymphocyte and in cancer progression, a transgenic T cell receptor mouse model specific to melanoma antigen hgp100 (pmel-1 TCR Tg) was established.

Depletion of both Dok1 and Dok2 did not affect the development, proliferation, mortality, activation and cytotoxic function of naive CD8+ T cells. However, after an in vitro pre-stimulation Dok1/Dok2 DKO CD8+ T cells had higher percentage of effector memory T cells and showed an increase in levels of pAKT and pERK upon TCR stimulation. Despite this improved TCR signaling, pre-stimulated Dok1/Dok2 DKO CD8+ T cells did not show any increase in their activation or cytotoxicity capacities against melanoma cell line expressing hgp100 in vitro.

Altogether we demonstrate here a novel aspect of the negative regulation by DOK1 and DOK2 proteins in CD8+ T cells. In conclusion, DOK1 and DOK2 have an inhibitory role following long term T cell stimulations.