Tag: pubmed

BMC Bioinformatics. 2022 Nov 8;23(1):469. doi: 10.1186/s12859-022-05012-2.

ABSTRACT

Early detection of cancers has been much explored due to its paramount importance in biomedical fields. Among different types of data used to answer this biological question, studies based on T cell receptors (TCRs) are under recent spotlight due to the growing appreciation of the roles of the host immunity system in tumor biology. However, the one-to-many correspondence between a patient and multiple TCR sequences hinders researchers from simply adopting classical statistical/machine learning methods. There were recent attempts to model this type of data in the context of multiple instance learning (MIL). Despite the novel application of MIL to cancer detection using TCR sequences and the demonstrated adequate performance in several tumor types, there is still room for improvement, especially for certain cancer types. Furthermore, explainable neural network models are not fully investigated for this application. In this article, we propose multiple instance neural networks based on sparse attention (MINN-SA) to enhance the performance in cancer detection and explainability. The sparse attention structure drops out uninformative instances in each bag, achieving both interpretability and better predictive performance in combination with the skip connection. Our experiments show that MINN-SA yields the highest area under the ROC curve scores on average measured across 10 different types of cancers, compared to existing MIL approaches. Moreover, we observe from the estimated attentions that MINN-SA can identify the TCRs that are specific for tumor antigens in the same T cell repertoire.

PMID:36348271 | DOI:10.1186/s12859-022-05012-2

Environ Sci Pollut Res Int. 2022 Nov 9. doi: 10.1007/s11356-022-23874-0. Online ahead of print.

ABSTRACT

To solve coordination between economic development and pollutant emissions, it is necessary to face the innovation problem of energy saving and emission reduction. Promoting the effective integration of tech and the financial system is an effective way to solve this problem. According to panel data for prefecture-level cities in China, this paper is based on the pilot policy of combining science and technology with finance implemented in 2011 as a quasi-natural experiment and uses the difference-in-differences (DID) method to evaluate the impact of Science and Technology Financial Policies (STFP) on the air pollutant emission, meanwhile, considering the spatial overflow effect of policy implementation. The research results show that: (1) The STFP has certain inhibitions on pollutant emissions, and this finding holds after a series of robustness tests. (2) The policy has different effects on cities that have different scale, different regions, and different government efficiency. (3) From the results of mechanism analysis, the policy mainly enhances regional pollutant emission reduction capacity through ways such as increasing regional green total factor productivity, enhancing regional science and technology levels, and promoting regional industrial structure optimization. (4) The policy shows a negative spatial spillover effect in reducing pollutant emissions.

PMID:36348242 | DOI:10.1007/s11356-022-23874-0

Health Justice. 2022 Nov 8;10(1):33. doi: 10.1186/s40352-022-00195-5.

ABSTRACT

BACKGROUND: The transition to the community after incarceration presents challenges for returning citizens, including the immediate need to secure housing, employment, and income. Additionally, health care is essential for this population due to high rates of chronic physical health and mental health problems and substance use disorders. There is growing recognition of the need for interventions that support returning citizens as they navigate community reintegration while simultaneously tending to physical and behavioral health needs. We developed and pilot tested a peer support intervention designed to provide social, emotional, and logistic support and promote linkage and engagement in healthcare for returning citizens. We tested the intervention with US military veterans in Massachusetts who were being released from prison and jail. Outcomes related to linkage to and engagement in healthcare were evaluated using an historical comparison group. Engagement in peer support, housing status, and reincarceration rates were monitored for the intervention group.

RESULTS: There were 43 veterans in the intervention group, and 36 in the historical comparison group. For linkage to primary care within 90 days of release, there were no statistically significant differences between the intervention and comparison groups (58% versus 67%). Intervention participants were significantly more likely to receive substance use treatment than the comparison group (86% versus 19%, p < .0001) and the mean monthly substance use visits was greater in the intervention group (0.96 versus 0.34, p < .007). Engagement in mental health services was greater for the intervention group than the comparison group (93% versus 64%, p < .003). There were no significant differences between groups for emergency department use and hospitalization. At the end of the study period, the majority of intervention participants who had been released for over a year were living in permanent housing (84%). Recidivism among the was low, with 7% re-arrested during the study period.

CONCLUSIONS: Augmenting reentry support through intensive peer support appears to have substantial benefits for veterans in terms of engaging them in health care and contributing to their longer-term stability, including housing and recidivism. Flexible reentry support such as this intervention may be well suited to meet the widely varying needs of returning citizens.

PMID:36348203 | DOI:10.1186/s40352-022-00195-5

J Racial Ethn Health Disparities. 2022 Nov 8. doi: 10.1007/s40615-022-01440-1. Online ahead of print.

ABSTRACT

BACKGROUND: Prior studies establish that Black neighborhoods and older persons experience higher rates of COVID-19 death than white neighborhoods and younger persons. However, such works point to the effect of age on COVID-19 mortality and the racial and ethnic inequalities present in COVID-19 deaths as independent vectors of inequality, neglecting to consider the multiplicative impact of structural conditions.

METHODS: Using weekly ZIP code counts of deaths from March 2020 through July 2021 from the Chicago Department of Public Health (n = 4168) and measures of structural characteristics derived from the 5-year estimates of the 2019 American Community Survey, the current study examined how place, racial composition, and the age structure of communities act in tandem to shape the number of deaths due to COVID-19. We used STATA to estimate negative binomial models predictive of COVID-19 mortality.

RESULTS: Findings from our statistical analysis revealed that in predominately Black neighborhoods, racial composition amplified the association of age structure (65 +) on COVID-19 mortality by 40%. Neighborhoods that were not predominately black did not show this multiplicative risk of death. Our findings underscore that the elevated risk of death in in older Black communities is attributed to historic and contemporary structural inequality.

CONCLUSIONS: Although society typically frames pandemics as natural disasters, doing such undermines dimensions of marginalization that amplify vulnerability among select populations. To begin eliminating such inequalities, the USA must deal with the entrenched limitations of institutions that render unequal attention and care to sectors of its population.

PMID:36348182 | DOI:10.1007/s40615-022-01440-1

Obes Surg. 2022 Nov 9. doi: 10.1007/s11695-022-06345-w. Online ahead of print.

ABSTRACT

INTRODUCTION: The inflammatory state that accompanies adiposity and the metabolic syndrome (MetS) is called “low-grade” inflammation. White blood cell count (WBC) has been proposed as an emerging biomarker for predicting future cardiovascular events, MetS and mortality. Bariatric surgery (BS) improves comorbidities associated with obesity and the MetS and the surgically induced weight loss is known to improve inflammatory status.

OBJECTIVES: To analyze the improvement of low-grade inflammation associated to obesity in patients with metabolically healthy severe obesity (MHSO) and patients with metabolically unhealthy obesity (MUSO) (severe obesity with MetS) after primary bariatric surgery as well as the protective effect of BS against the development of MetS in patients with MHSO by reducing the WBC.

MATERIALS AND METHODS: Retrospective analysis of prospectively collected data of patients undergoing laparoscopic primary BS (gastric by-pass or sleeve gastrectomy) from January 2004-December 2015. Outcomes included changing of low-grade inflammation in terms of leukocytes, neutrophils, lymphocytes, and platelets.

RESULTS: Twenty-one patients with MHSO and 167 patients with MUSO underwent laparoscopic primary BS. The preoperative values of leukocyte and platelet were statistically higher in the group of patients with MHSO. In both groups, there was significant postoperative decrease of inflammatory markers. The greatest drop in WBC occurred in the second postoperative year. No patient of the group of patients with MHSO developed MetS within five postoperative years.

CONCLUSIONS: Surgically induced weight loss plays an important role for improvement in chronic inflammation associated to obesity because of reduction of visceral fat mass. MHSO associates a low-grade chronic inflammatory status comparable to MUSO. The improvement or decrease of low-grade inflammation in patients with metabolically healthy severe obesity after bariatric surgery could have a protective effect against the development of MetS and medical conditions associated with severe obesity.

PMID:36348177 | DOI:10.1007/s11695-022-06345-w

Med Biol Eng Comput. 2022 Nov 8. doi: 10.1007/s11517-022-02703-z. Online ahead of print.

ABSTRACT

Medical images of patients must be securely transmitted and kept private in telemedicine. To secure such medical images, this paper proposes a single round chaotic image encryption scheme based on a permutation-diffusion structure. A combined chaotic key generator (CCKG) is proposed to enhance key sensitivity and generation in order to improve the security of medical images to be encrypted. CCKG is used to produce the initial seeds for the fractional order chaotic system (FOCS) and Lorenz system (LS) for the permutation and diffusion processes, respectively. CCKG together with proposed permutation and diffusion methods enhances cipher image security in single round. Using zigzag transform (ZT) scanning, the plain image is first permuted block by block. The type of scanning used on each block is heavily influenced by the ZT selection from FOCS and LS. Following block-wise permutation, the permutation order (PO) generated from LS performs overall permutation. Based on the pixel positions, the overall permuted image is divided into odd and even parts. Then these parts of the images are diffused separately by the random pixel matrices generated by LS and FOCS. The cipher image is formed by combining the odd and even parts after diffusion. Secret key analysis, statistical analysis, differential attack analysis, and simulations confirm that with a single round of image encryption, the proposed system is competent, robust and effective.

PMID:36348143 | DOI:10.1007/s11517-022-02703-z

Results Probl Cell Differ. 2022;70:103-156. doi: 10.1007/978-3-031-06573-6_4.

ABSTRACT

What holds together the world in its innermost, what life is, how it emerges, functions, and evolves, has not only been an epic matter of endless romantic sunset poetry and philosophy, but also manifests explicitly in its perhaps most central organization unit-genomes. Their 3D architecture and dynamics, including the interaction networks of regulatory elements, obviously co-evolved as inseparable systems allowing the physical storage, expression, and replication of genetic information. Since we were able to fill finally the much-debated centennial gaps in their 3D architecture and dynamics, now entire new perspectives open beyond epigenetics reaching as far as a general understanding of living systems: besides the previously known DNA double helix and nucleosome structure, the latter compact into a chromatin quasi-fibre folded into stable loops forming stable multi-loop aggregates/rosettes connected by linkers, creating hence the again already known chromosome arms and entire chromosomes forming the cell nucleus. Instantly and for the first time this leads now to a consistent and cross-proven systems statistical mechanics genomics framework elucidating genome intrinsic function and regulation including various components. It balances stability/flexibility ensuring genome integrity, enabling expression/regulation of genetic information, as well as genome replication/spread. Furthermore, genotype and phenotype are multiplisticly entangled being evolutionarily the outcome of both Darwinian natural selection and Lamarckian self-referenced manipulation-all embedded in even broader genome ecology (autopoietic) i(!)n- and environmental scopes. This allows formulating new meta-level functional semantics of genomics, i.e. notions as communication of genes, genomes, and information networks, architectural and dynamic spaces for creativity and innovation, or genomes as central geno-/phenotype entanglements. Beyond and most fundamentally, the paradoxical-seeming local equilibrium substance stability in its entity though far from a universal heat-death-like equilibrium is solved, and system irreversibility, time directionality, and thus the emergence of existence are clarified. Consequently, real deep understandings of genomes, life, and complex systems in general appear in evolutionary perspectives as well as from systems analyses, via system damage/disease (its repair/cure and manipulation) as far as the understanding of extraterrestrial life, the de novo creation and thus artificial life, and even the raison d’etre.

PMID:36348106 | DOI:10.1007/978-3-031-06573-6_4

Results Probl Cell Differ. 2022;70:35-69. doi: 10.1007/978-3-031-06573-6_2.

ABSTRACT

The purpose of our studies is to elucidate the nature of massive control of the whole genome expression with a particular emphasis on cell-fate change. The whole genome expression is coordinated by the emergence of a critical point (CP: a peculiar set of biphasic genes) with the genome acting as an integrated dynamical system. In response to stimuli, the genome expression self-organizes into local sub-, near-, and super-critical states, each exhibiting distinct collective behaviors with its center of mass acting as a local attractor, coexisting with the whole genome attractor (GA). The CP serves as the organizing center of cell-fate change, and its activation makes local perturbation to spread over the genome affecting GA. The activation of CP is in turn elicited by genes with elevated temporal variance (oscillating-mode genes), normally in charge to keep genome expression at pace with microenvironment fluctuations. When oscillation exceeds a given threshold, the CP synchronizes with the GA driving genome expression state transition. The expression synchronization wave invading the entire genome is fostered by the fusion-splitting dynamics of silencing pericentromere-associated heterochromatin domains and the consequent folding-unfolding transitions of transcribing euchromatin domains. The proposed mechanism is a unified step toward a time-evolutional transition theory of biological regulation.

PMID:36348104 | DOI:10.1007/978-3-031-06573-6_2

Aesthetic Plast Surg. 2022 Nov 8. doi: 10.1007/s00266-022-03154-5. Online ahead of print.

ABSTRACT

BACKGROUND: Small-incisional double-eyelid surgery has increasingly gained popularity. In the published studies, the number of incisions, the debulking method, and the pretarsal fixation differ significantly among studies. Hence, this article was conducted to summarize the different techniques and compare their surgical results and complications.

METHODS: The literature review was conducted using the PubMed and Cochrane databases from their inception to June 1, 2022. Clinical studies of small-incisional blepharoplasty with available full-text and extractable data were included and were grouped depending on the number of incisions. The number, length and location of the incisions, debulking method, fixation technique, and skin closure were concluded. The complications were statistically analyzed and compared.

RESULTS: Finally, 13 articles and 4177 patients were eligible for reviewing, among which 5 studies (2460 patients) described single-incisional technique, 2 studies (645 patients) described two-incisional technique, 5 studies (700 patients) described three-incisional technique, and 1 study (372 patients) described four-incisional technique. Through the small incisions, the pretarsal soft tissue can be removed as appropriate, and the pretarsal fixation can be firm and exact. Both the single- and three-incisional studies had a pooled total complication rate of 5% and a pooled foldloss rate of 2%. No significant difference was found between groups.

CONCLUSIONS: The small-incisional techniques offer a simple, safe, and reproducible approach to double-eyelids. It reduces post-op recovery time and allows a tenacious fixation. The fold-loss rate and other complication rate are acceptable when compared with the non-incisional and full-incisional techniques.

LEVEL OF EVIDENCE III: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

PMID:36348097 | DOI:10.1007/s00266-022-03154-5

J Appl Clin Med Phys. 2022 Nov 8:e13806. doi: 10.1002/acm2.13806. Online ahead of print.

ABSTRACT

PURPOSE: This manuscript describes the structure, management and outcomes of a multi-institutional clinical and research medical physics residency program (Harvard Medical Physics Residency Program, or HMPRP) to provide potentially useful information to the centers considering a multi-institutional approach for their training programs.

METHODS: Data from the program documents and public records was used to describe HMPRP and obtain statistics about participating faculty, enrolled residents, and graduates. Challenges associated with forming and managing a multi-institutional program and developed solutions for effective coordination between several clinical centers are described.

RESULTS: HMPRP was formed in 2009 and was accredited by the Commission on Accreditation of Medical Physics Education Programs (CAMPEP) in 2011. It is a 3-year therapy program, with a dedicated year of research and the 2 years of clinical training at three academic hospitals. A CAMPEP-accredited Certificate Program is embedded in HMPRP to allow enrolled residents to complete a formal didactic training in medical physics if necessary. The clinical training covers the material required by CAMPEP. In addition, training in protons, CyberKnife, MR-linac, and at network locations is included. The clinical training and academic record of the residents is outstanding. All graduates have found employment within clinical medical physics, mostly at large academic centers and graduates had a 100% pass rate at the oral American Board of Radiology exams. On average, three manuscripts per resident are published during residency, and multiple abstracts are presented at conferences.

CONCLUSIONS: A multi-institutional medical physics residency program can be successfully formed and managed. With a collaborative administrative structure, the program creates an environment for high-quality clinical training of the residents and high productivity in research. The main advantage of such program is access to a wide variety of resources. The main challenge is creating a structure for efficient management of multiple resources at different locations. This report may provide valuable information to centers considering starting a multi-institutional residency program.

PMID:36347055 | DOI:10.1002/acm2.13806