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1.
Heliyon ; 10(11): e31958, 2024 Jun 15.
Article En | MEDLINE | ID: mdl-38868046

Multi-drug resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a global health threat. The severity of the problem lies in its impact on mortality, therapeutic limitations, the threat to public health, and the costs associated with managing infections caused by these resistant strains. Effectively addressing this challenge requires innovative approaches to research, the development of new antimicrobials, and more responsible antibiotic use practices globally. Antimicrobial peptides (AMPs) are a part of the innate immune system of all higher organisms. They are short, cationic and amphipathic molecules with broad-spectrum activity. AMPs interact with the negatively charged bacterial membrane. In recent years, AMPs have attracted considerable interest as potential antibiotics. However, AMPs have low bioavailability and short half-lives, which may be circumvented by chemical modification. This review presents recent in vitro and in silico strategies for the modification of AMPs to improve their stability and application in preclinical experiments.

3.
Brain Behav Immun ; 120: 151-158, 2024 May 20.
Article En | MEDLINE | ID: mdl-38777283

OBJECTIVE: This epigenomics sub-study embedded within a randomized controlled trial examined whether an evidenced-based behavioral intervention model that decreased stimulant use altered leukocyte DNA methylation (DNAm). METHODS: Sexual minority men with HIV who use methamphetamine were randomized to a five-session positive affect intervention (n = 32) or an attention-control condition (n = 21), both delivered during three months of contingency management for stimulant abstinence. All participants exhibited sustained HIV virologic control - an HIV viral load less than 40 copies/mL at baseline and six months post-randomization. The Illumina EPIC BeadChip measured leukocyte methylation of cytosine-phosphate-guanosine (CpG) sites mapping onto five a priori candidate genes of interest (i.e., ADRB2, BDNF, FKBP5, NR3C1, OXTR). Functional DNAm pathways and soluble markers of immune dysfunction were secondary outcomes. RESULTS: Compared to the attention-control condition, the positive affect intervention significantly decreased methylation of CpG sites on genes that regulate ß2 adrenergic and oxytocin receptors. There was an inconsistent pattern for the direction of the intervention effects on methylation of CpG sites on genes for glucocorticoid receptors and brain-derived neurotrophic factor. Pathway analyses adjusting for the false discovery rate (padj < 0.05) revealed significant intervention-related alterations in DNAm of Reactome pathways corresponding to neural function as well as dopamine, glutamate, and serotonin release. Positive affect intervention effects on DNAm were accompanied by significant reductions in the self-reported frequency of stimulant use. CONCLUSIONS: There is an epigenetic signature of an evidence-based behavioral intervention model that reduced stimulant use, which will guide the identification of biomarkers for treatment responses.

4.
AIDS ; 2024 Apr 12.
Article En | MEDLINE | ID: mdl-38608008

OBJECTIVE: Adolescents with perinatally-acquired HIV (AWH) are at an increased risk of poor cognitive development but the underlying mechanisms remain unclear. Circulating galectin-9 (Gal-9) has been associated with increased inflammation and multi-morbidity in adults with HIV despite anti-retroviral therapy (ART), however, relationship between Gal-9 in AWH and cognition remain unexplored. DESIGN: A cross-sectional study of two independent age-matched cohorts from India [AWH on ART (n = 15), ART-naïve (n = 15), and adolescents without HIV (AWOH; n = 10)] and Myanmar [AWH on ART (n = 54) and AWOH (n = 22)] were studied. Adolescents from Myanmar underwent standardized cognitive tests. METHODS: Plasma Gal-9 and soluble mediators were measured by immunoassays and cellular immune markers by flow cytometry. We used Mann-Whitney U tests to determine group-wise differences, Spearman's correlation for associations and machine learning (ML) to identify a classifier of cognitive status (impaired vs. unimpaired) built from clinical (age, sex, HIV status) and immunological markers. RESULTS: Gal-9 levels were elevated in ART-treated AWH compared to AWOH in both cohorts (all p < 0.05). Higher Gal-9 in AWH correlated with increased levels of inflammatory mediators (sCD14, TNFα, MCP-1, IP-10, IL-10) and activated CD8 T cells (all p < 0.05). Irrespective of HIV status, higher Gal-9 levels correlated with lower cognitive test scores in multiple domains (verbal learning, visuospatial learning, memory, motor skills (all p < 0.05). ML classification identified Gal-9, CTLA-4, HVEM, and TIM-3 as significant predictors of cognitive deficits in adolescents (mean AUC = 0.837). CONCLUSION: Our results highlight a potential role of Gal-9 as a biomarker of inflammation and cognitive health among adolescents with perinatally acquired HIV.

5.
Res Sq ; 2024 Apr 03.
Article En | MEDLINE | ID: mdl-38645141

Background: Hepatitis C virus (HCV) coinfection may further compromise immunological and cognitive function in people with HIV (PWH). This study compared laboratory and neuropsychiatric measures across the periods of HCV seroconversion and direct-acting antiviral (DAA) therapy with sustained virologic response (SVR) among PWH who initiated antiretroviral therapy (ART) during acute HIV infection (AHI) and acquired HCV after 24 weeks of ART. Methods: Participants from the RV254 AHI cohort underwent paired laboratory and neuropsychiatric assessments during regular follow-up. The former included measurements of CD4 + and CD8 + T-cell counts, HIV RNA, liver enzymes, and lipid profiles. The latter included the Patient Health Questionnaire-9 (PHQ-9), Distress Thermometer (DT), and a 4-test cognitive battery that evaluated psychomotor speed, executive function, fine motor speed and dexterity. The raw scores in the battery were standardized and averaged to create an overall performance (NPZ-4) score. Parameters of HCV-coinfected participants were compared across HCV seroconversion and DAA treatment groups. Results: Between 2009 and 2022, 79 of 703 RV254 participants acquired HCV after ≥ 24 weeks of ART; 53 received DAA, and 50 (94%) achieved SVR. All participants were Thai males (median age: 30 years); 34 (68%) denied past intravenous drug use, and 41 (82%) had a history of other sexually transmitted infections during follow-up. Following SVR, aspartate transferase (AST) and alanine transaminase (ALT) decreased (p < 0.001), while total cholesterol, low-density lipoprotein, and triglycerides increased (p < 0.01). The median CD4+/CD8 + ratio increased from 0.91 to 0.97 (p = 0.012). NPZ-4 improved from 0.75 to 0.91 (p = 0.004). The median DT score increased from 1.7 to 2.7 (p = 0.045), but the PHQ-9 score remained unchanged. Conclusion: HCV coinfection is common in this group of high-risk PWH, highlighting the need for regular screening, early diagnosis, and treatment. There was a modest improvement in the CD4+/CD8 + T-cell ratio and cognitive performance after DAA therapy in patients who achieved SVR. Future studies should examine potential neuropsychiatric impacts during early HCV infection as well as the longer-term neuropsychiatric outcomes after DAA treatment with SVR.

6.
PLOS Glob Public Health ; 4(3): e0002941, 2024.
Article En | MEDLINE | ID: mdl-38502635

Qualitative research approaches were used to launch an international research collaboration between the U. S. and Cambodia. Cambodian officials requested assistance in learning qualitative approaches to complement the research skills of Cambodian mental health providers. This article provides a description of how U. S. researchers responded to that request and engaged with Cambodian psychiatrists to explore mental health needs and interventions in both countries and initiate a sustainable relationship. The early focus on qualitative research methodologies may be an avenue that mitigates some of the challenges that can characterize international research. In this study, early communications involved developing a plan to teach qualitative methods while also collecting and analyzing data in both countries that would address the mental health concerns experienced by respective care providers. A case study exemplar was embedded with a scripted focus group guide to collect data from U. S. focus groups, then share with Cambodian psychiatrists. Components of hermeneutic phenomenological interviewing and descriptive content analysis were used to simultaneously teach and enact the research methods, gather data in both countries to analyze, and inspire participants to replicate the methods in their ongoing work. Cambodian psychiatrists were able to demonstrate competence in facilitating focus groups after being participant-observers. Researcher/practitioners from both U. S. and Cambodian teams gained new understandings about the mental health needs of their patients. The mutual engagement of a research focus is an effective way to establish cross-cultural relationships. The challenges of staying with stable teams over times remain, but the content shared and learned in a participatory structure yields understandings that cross cultural boundaries. Anticipated and unexpected challenges may be offset by an intention of reciprocity and mutual engagement. The use of qualitative methodologies, early and repeatedly, can facilitate relational understanding.

7.
Pediatr Radiol ; 2024 Mar 11.
Article En | MEDLINE | ID: mdl-38462578

Germ cell tumors of childhood are tumors arising from germline cells in gonadal or extragonadal locations. Extragonadal germ cell tumors are characteristically located in the midline, arising intracranially or in the mediastinum, retroperitoneum, or pelvis. These tumors are generally easily diagnosed due to typical sites of origin, characteristic imaging findings, and laboratory markers. However, germ cell tumors can be associated with unusual clinical syndromes or imaging features that can perplex the radiologist. This review will illustrate atypical imaging/clinical manifestations and complications of abdominal germ cell tumors in childhood. These features include unusual primary tumors such as multifocal primaries; local complications such as ovarian torsion or ruptured dermoid; atypical presentations of metastatic disease associated with burned-out primary tumor, growing teratoma syndrome, and gliomatosis peritonei; endocrine manifestations such as precocious puberty and hyperthyroidism; and antibody mediated paraneoplastic syndrome such as anti-N-methyl-D-aspartate-receptor antibody-mediated encephalitis. This review aims to illustrate unusual imaging features associated with the primary tumor, metastatic disease, or distant complications of abdominal germ cell tumors of childhood.

8.
AIDS Behav ; 28(6): 1811-1821, 2024 Jun.
Article En | MEDLINE | ID: mdl-38493283

The growing number of people aging with HIV represents a group vulnerable to the symptom burdens of HIV-associated neurocognitive disorder (HAND). Among younger groups, Mindfulness-Based Stress Reduction (MBSR) has been shown to help people living with HIV manage HIV-related and other life stress, and although there is some theoretical and empirical evidence that it may be effective among those with cognitive deficits, the approach has not been studied in older populations with HAND. Participants (n = 180) 55 years or older with HIV and cognitive impairment were randomly assigned to either an 8-week MBSR arm or a waitlist control. We assessed the impact of MBSR compared to a waitlist control on psychological outcomes [stress, anxiety, depression, and quality of life (QOL)] and cognitive metrics (e.g., speed of information processing, working memory, attention, impulsivity) measured at baseline, immediately post intervention (8 weeks) and one month later (16 weeks). Intent to treat analyses showed significant improvement in the MBSR group compared to control on symptoms of depression from baseline to 8 weeks, however, the difference was not sustained at 16 weeks. The MBSR group also showed improvement in perceived QOL from baseline to 16 weeks compared to the waitlist control group. Cognitive performance did not differ between the two treatment arms. MBSR shows promise as a tool to help alleviate the symptom burden of depression and low QOL in older individuals living with HAND and future work should address methods to better sustain the beneficial impact on depression and QOL.


Depression , HIV Infections , Mindfulness , Quality of Life , Stress, Psychological , Humans , Male , Female , Middle Aged , HIV Infections/psychology , HIV Infections/complications , Stress, Psychological/therapy , Stress, Psychological/psychology , Depression/therapy , Depression/psychology , Aged , Treatment Outcome , Anxiety/psychology , Anxiety/therapy , Cognitive Dysfunction/therapy , Cognitive Dysfunction/psychology
9.
Alzheimers Dement (N Y) ; 10(1): e12452, 2024.
Article En | MEDLINE | ID: mdl-38356474

INTRODUCTION: Heterozygous mutations in the GRN gene lead to reduced progranulin (PGRN) levels in plasma and cerebrospinal fluid (CSF) and are causative of frontotemporal dementia (FTD) with > 90% penetrance. Latozinemab is a human monoclonal immunoglobulin G1 antibody that is being developed to increase PGRN levels in individuals with FTD caused by heterozygous loss-of-function GRN mutations. METHODS: A first-in-human phase 1 study was conducted to evaluate the safety, tolerability, pharmacokinetics (PK), and pharmacodynamics (PD) of multiple-dose intravenous administration of latozinemab in eight symptomatic participants with FTD caused by a heterozygous loss-of-function GRN mutation (FTD-GRN). RESULTS: Latozinemab demonstrated favorable safety and PK/PD profiles. Multiple-dose administration of latozinemab increased plasma and CSF PGRN levels in participants with FTD-GRN to levels that approximated those seen in healthy volunteers. DISCUSSION: Data from the first-in-human phase 1 study support further development of latozinemab for the treatment of FTD-GRN. Highlights: GRN mutations decrease progranulin (PGRN) and cause frontotemporal dementia (FTD).Latozinemab is being developed as a PGRN-elevating therapy.Latozinemab demonstrated a favorable safety profile in a phase 1 clinical trial.Latozinemab increased PGRN levels in the CNS of symptomatic FTD-GRN participants.

10.
AIDS Behav ; 28(2): 695-704, 2024 Feb.
Article En | MEDLINE | ID: mdl-38281251

Loneliness among older adults has been identified as a major public health problem. Yet little is known about loneliness, or the potential role of social networks in explaining loneliness, among older people with HIV (PWH) in sub-Saharan Africa, where 70% of PWH reside. To explore this issue, we analyzed data from 599 participants enrolled in the Quality of Life and Ageing with HIV in Rural Uganda study, including older adults with HIV in ambulatory care and a comparator group of people without HIV of similar age and gender. The 3-item UCLA Loneliness Scale was used to measure loneliness, and HIV status was the primary explanatory variable. The study found no statistically significant correlation between loneliness and HIV status. However, individuals with HIV had smaller households, less physical and financial support, and were less socially integrated compared to those without HIV. In multivariable logistic regressions, loneliness was more likely among individuals who lived alone (aOR:3.38, 95% CI:1.47-7.76) and less likely among those who were married (aOR:0.34, 95% CI:0.22-0.53) and had a higher level of social integration (aOR:0.86, 95% CI: 0.79-0.92). Despite having smaller social networks and less support, older adults with HIV had similar levels of loneliness as those without HIV, which may be attributed to resiliency and access to HIV-related health services among individuals with HIV. Nonetheless, further research is necessary to better understand the mechanisms involved.


HIV Infections , Loneliness , Humans , Aged , Quality of Life , Uganda/epidemiology , HIV Infections/epidemiology , Social Networking
11.
AIDS ; 38(3): 373-378, 2024 Mar 01.
Article En | MEDLINE | ID: mdl-37916464

OBJECTIVE: HIV-1 invades the brain within days post-transmission. This study quantitated cerebrospinal fluid (CSF) white blood cell count (WBC) and investigated whether it associated with plasma and CSF HIV-1 RNA during untreated acute HIV infection (AHI). DESIGN: Seventy participants underwent lumbar puncture during Fiebig stages I-V AHI. METHOD: WBC and HIV-1 RNA with a lower limit of quantification (LLQ) of 80 copies/ml were measured in CSF. RESULTS: Sixty-nine (99%) participants were men, with a median age of 26. Their blood CD4 + and CD8 + T-cell counts were 335 [interquartile range (IQR) 247-553) and 540 (IQR 357-802) cells/µl, respectively. Forty-five (64%) were in Fiebig stages III-V whereas 25 (36%) were in Feibig stages I-II. Fifty-two (74%) experienced acute retroviral syndrome. Median plasma and CSF HIV-1 RNA were 6.10 (IQR 5.15-6.78) and 3.15 (IQR 1.90-4.11) log 10 copies/ml, respectively. Sixteen (23%) CSF samples had HIV-1 RNA below LLQ. Median CSF WBC was 2.5 (IQR 1-8) cells/µl. CSF pleocytosis (WBC >5) was observed in 33% and was only present in CSF samples with detectable HIV-1 RNA. The frequencies of CSF pleocytosis during Fiebig stages III-V and among CSF samples of higher viral load (>1000 copies/ml) were 42 and 45%, respectively. Pleocytosis independently associated with CSF HIV-1 RNA in multivariate analysis [adjusted coefficient: 0.79, 95% confidence interval (CI) 0.41-1.14), P  < 0.001] and a lower plasma to CSF HIV-1 RNA ratio ( P  < 0.001). CONCLUSION: CSF pleocytosis was present in one-third of participants with AHI. It associated with higher CSF HIV-1 RNA and a lower plasma to CSF HIV-1 RNA ratio, suggesting a potential association with HIV-1 neuroinvasion.


HIV Infections , HIV Seropositivity , HIV-1 , Male , Humans , Female , HIV Infections/complications , HIV-1/genetics , Leukocytosis , HIV Seropositivity/complications , RNA, Viral , Viral Load , Cerebrospinal Fluid
12.
Methods Mol Biol ; 2746: 1-20, 2024.
Article En | MEDLINE | ID: mdl-38070076

The mitochondria are essential to eukaryotic life, acting as key drivers of energy generation while also being involved in the regulation of many cellular processes including apoptosis, cell proliferation, calcium homeostasis, and metabolism. Mitochondrial diseases which disrupt these processes lead to a diverse range of pathologies and lack consistency in symptom presentation. In disease, mitochondrial activity and energy homeostasis can be adapted to cellular requirements, and studies using Dictyostelium and human lymphoblastoid cell lines have shown that such changes can be facilitated by the key cellular and energy regulators, TORC1 and AMPK. Fluorescence-based assays are increasingly utilized to measure mitochondrial and cell signalling function in mitochondrial disease research. Here, we describe a streamlined method for the simultaneous measurement of mitochondrial mass, membrane potential, and reactive oxygen species production using MitoTracker Green™ FM, MitoTracker Red™ CMXRos, and DCFH-DA probes. This protocol has been adapted for both Dictyostelium and human lymphoblastoid cell lines. We also describe a method for assessing TORC1 and AMPK activity simultaneously in lymphoblastoid cells. These techniques allow for the characterization of mitochondrial defects in a rapid and easy to implement manner.


Dictyostelium , Mitochondrial Diseases , Humans , AMP-Activated Protein Kinases/metabolism , Dictyostelium/metabolism , Mitochondria/metabolism , Mitochondrial Diseases/metabolism , Reactive Oxygen Species/metabolism , Phenotype , Mechanistic Target of Rapamycin Complex 1/metabolism
13.
Clin Infect Dis ; 78(6): 1608-1616, 2024 Jun 14.
Article En | MEDLINE | ID: mdl-38147306

BACKGROUND: Older people with human immunodeficiency virus (HIV, PWH) are prone to using multiple medications due to higher rates of medical comorbidities and the use of antiretroviral therapy (ART). We assessed the prevalence and clinical impact of polypharmacy among PWH. METHODS: We leveraged clinical data from the AIDS Clinical Trials Group A5322 study "Long-Term Follow-up of Older HIV-infected Adults: Addressing Issues of Aging, HIV Infection and Inflammation" (HAILO). We included PWH aged ≥40 years with plasma HIV RNA levels <200 copies/µL. We assessed the relationship between polypharmacy (defined as the use of 5 or more prescription medications, excluding ART) and hyperpolypharmacy (defined as the use of 10 or more prescription medications, excluding ART) with slow gait speed (less than 1 meter/second) and falls, including recurrent falls. RESULTS: Excluding ART, 24% of study participants had polypharmacy and 4% had hyperpolypharmacy. Polypharmacy was more common in women (30%) than men (23%). Participants with polypharmacy had a higher risk of slow gait speed (odds ratio [OR] = 1.78; 95% confidence interval [CI] = 1.27-2.50) and increased risk of recurrent falls (OR = 2.12; 95% CI = 1.06-4.23). The risk for recurrent falls was further increased in those with hyperpolypharmacy compared with those without polypharmacy (OR = 3.46; 95% CI = 1.32-9.12). CONCLUSIONS: In this large, mixed-sex cohort of PWH aged ≥40 years, polypharmacy was associated with slow gait speed and recurrent falls, even after accounting for medical comorbidities, alcohol use, substance use, and other factors. These results highlight the need for increased focus on identifying and managing polypharmacy and hyperpolypharmacy in PWH.


Accidental Falls , HIV Infections , Polypharmacy , Humans , Male , Female , HIV Infections/drug therapy , HIV Infections/complications , Accidental Falls/statistics & numerical data , Middle Aged , Aged , Walking Speed , Adult , Comorbidity , Risk Factors
14.
Curr HIV/AIDS Rep ; 20(6): 321-332, 2023 Dec.
Article En | MEDLINE | ID: mdl-37971597

PURPOSE OF REVIEW: In the era of HIV treatment as prevention (TasP), more clarity is needed regarding whether people with HIV who use stimulants (i.e., methamphetamine, powder cocaine, and crack cocaine) display elevated HIV viral load and greater immune dysregulation. RECENT FINDINGS: Although rates of viral suppression have improved in the TasP era, stimulant use was independently associated with elevated viral load in 23 of 28 studies included in our review. In the 12 studies examining other HIV disease markers, there was preliminary evidence for stimulant-associated alterations in gut-immune dysfunction and cellular immunity despite effective HIV treatment. Studies generally focused on documenting the direct associations of stimulant use with biomarkers of HIV pathogenesis without placing these in the context of social determinants of health. Stimulant use is a key barrier to optimizing the effectiveness of TasP. Elucidating the microbiome-gut-brain axis pathways whereby stimulants alter neuroimmune functioning could identify viable targets for pharmacotherapies for stimulant use disorders. Examining interpersonal, neighborhood, and structural determinants that could modify the associations of stimulant use with biomarkers of HIV pathogenesis is critical to guiding the development of comprehensive, multi-level interventions.


Central Nervous System Stimulants , HIV Infections , Humans , Acquired Immunodeficiency Syndrome/drug therapy , Biomarkers , Central Nervous System Stimulants/adverse effects , Crack Cocaine/adverse effects , HIV Infections/pathology , Methamphetamine/adverse effects
15.
Psychoanal Q ; 92(3): 377-405, 2023.
Article En | MEDLINE | ID: mdl-38032759

In this paper, I present a new reading of Erik Erikson's theory of epigenetic stages of development, with particular attention to the concept of identity. I show that Erikson's psychosocial approach requires close attention to the role of the community in the formation of individual identity and to the importance of the stage of generativity as an often overlooked component in understanding both identity and the whole Eriksonian life cycle.


Epigenomics , Psychoanalytic Theory , Humans
16.
Int Med Case Rep J ; 16: 767-773, 2023.
Article En | MEDLINE | ID: mdl-38020582

Intraosseous schwannoma is a rare diagnosis, particularly so in the skull. Accordingly, little data exists to unify common features of this disease. Here, we present the fourth known case of a primary intraosseous schwannoma of the frontal bone: a 46-year-old male with severe, progressive headache and an osteolytic frontal bone lesion. Gross total resection of the lesion was performed with excellent clinical outcome. Histological analysis confirmed the diagnosis. The limited existing literature on this topic was reviewed to identify emerging trends surrounding presenting symptoms and treatment. Early literature suggests symptoms are often nonspecific, except for lesions of the petrous apex. No cases of recurrence have been demonstrated after gross total resection, though incomplete resection has been associated with recurrence. This diagnosis appears to be becoming a more often-considered differential for osteolytic, expansile skull lesions.

17.
Plast Reconstr Surg Glob Open ; 11(9): e5261, 2023 Sep.
Article En | MEDLINE | ID: mdl-37691708

Background: Seroma, along with other complications, occurs as a result of poor wound healing following breast reconstructive surgery. The Interi System was developed to address the need for more effective approaches to close internal dead space and evacuate postsurgical fluid. Interi is an internal negative pressure delivery system with a unique branching manifold for broad coverage of internal tissue planes. Initial experience in a small cohort undergoing prepectoral breast reconstruction showed a clinical and statistically significant reduction in seroma and any complication versus standard drains. The purpose of this study is to report on the safety and effectiveness of Interi, compared with standard drains, in a larger patient population followed up over a longer period than our initial study. Methods: Data on demographics, mastectomy and reconstructive variables, postoperative complications, and manifold/drain duration were retrieved from patient records and compared between the two groups. Results: Interi was used in 100 patients (170 breasts) and standard drains in 100 patients (166 breasts). Groups were well matched in demographic, reconstructive, and mastectomy variables. Interi was removed significantly earlier than drains (16.5 versus 19.6 days; P < 0.0001) and was associated with a significantly lower incidence of seroma (4.1% versus 22.9%, P < 0.00001), flap revision (10.6% versus 21.7%, P = 0.006), and any complication (23.5% versus 44.0%, P = 0.0001). Conclusions: Interi effectively reduced dead space and evacuated fluid from internal tissue planes, thereby decreasing seroma and other complications after prepectoral breast reconstruction. As a viable alternative to standard drains, it could significantly improve patient outcomes.

18.
Mol Cell Biochem ; 2023 Aug 23.
Article En | MEDLINE | ID: mdl-37610616

The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across various organisms. The first comprehensive genome sequencing of E. coli K12 revealed that more than 50% of its open reading frames corresponded to transcripts with no known functions. The group of protein-coding genes without a functional description and/or a recognized pathway, beginning with the letter "Y", is classified as the "y-ome". Several efforts have been made to elucidate the functions of these genes and to recognize their role in biological processes. This review provides a brief update on various strategies employed when studying the y-ome, such as high-throughput experimental approaches, comparative omics, metabolic engineering, gene expression analysis, and data integration techniques. Additionally, we highlight recent advancements in functional annotation methods, including the use of machine learning, network analysis, and functional genomics approaches. Novel approaches are required to produce more precise functional annotations across the genome to reduce the number of genes with unknown functions.

19.
Drug Alcohol Depend ; 251: 110942, 2023 10 01.
Article En | MEDLINE | ID: mdl-37651812

BACKGROUND: Sexual minority men (SMM) report high rates of stimulant use (e.g., crystal methamphetamine, cocaine) and HIV infection. Stimulant use contributes to immune dysfunction, which enhances risk for HIV acquisition and pathogenesis. Research is needed to examine the independent and interactive relationships of stimulant use and HIV infection with systemic immune dysregulation among SMM, especially during the COVID-19 pandemic. METHODS: From 2020-2022, 75 SMM in Miami, Florida with and without HIV completed an online survey and provided biospecimens to assess HIV status and viral load (VL), recent stimulant use, and soluble markers of immune activation and inflammation in plasma, including soluble CD14 (sCD14) and elevated high-sensitivity C-reactive protein (hs-CRP > 1.0mg/L). Sociodemographics and prior SARS-CoV-2 infection were compared across HIV status/stimulant use groups. Moderation models examined the independent and interactive associations of stimulant use and HIV status with sCD14 and elevated hs-CRP. RESULTS: Thirty participants were persons living with HIV (PWH) (50% with stimulant use), and 45 were HIV-negative (44% with stimulant use). SARS-CoV-2 infection was not associated with stimulant use/HIV groups or immune outcomes. HIV-negative SMM without stimulant use had lower sCD14 compared to other SMM, as well as lower odds of elevated hs-CRP compared to PWH who used stimulants. Stimulant use showed independent associations with immune dysregulation that persisted after controlling for HIV status and VL, whereas HIV status was only independently associated with elevated hs-CRP in one model not controlling for VL. CONCLUSIONS: Among SMM, stimulant use was independently associated with elevated immune activation and inflammation.


COVID-19 , HIV Infections , Sexual and Gender Minorities , Male , Humans , HIV Infections/epidemiology , HIV Infections/complications , C-Reactive Protein , Lipopolysaccharide Receptors , Pandemics , SARS-CoV-2 , Inflammation , Homosexuality, Male
20.
Nature ; 620(7974): 557-561, 2023 Aug.
Article En | MEDLINE | ID: mdl-37587300

Supercooled water droplets are widely used to study supercooled water1,2, ice nucleation3-5 and droplet freezing6-11. Their freezing in the atmosphere affects the dynamics and climate feedback of clouds12,13 and can accelerate cloud freezing through secondary ice production14-17. Droplet freezing occurs at several timescales and length scales14,18 and is sufficiently stochastic to make it unlikely that two frozen drops are identical. Here we use optical microscopy and X-ray laser diffraction to investigate the freezing of tens of thousands of water microdrops in vacuum after homogeneous ice nucleation around 234-235 K. On the basis of drop images, we developed a seven-stage model of freezing and used it to time the diffraction data. Diffraction from ice crystals showed that long-range crystalline order formed in less than 1 ms after freezing, whereas diffraction from the remaining liquid became similar to that from quasi-liquid layers on premelted ice19,20. The ice had a strained hexagonal crystal structure just after freezing, which is an early metastable state that probably precedes the formation of ice with stacking defects8,9,18. The techniques reported here could help determine the dynamics of freezing in other conditions, such as drop freezing in clouds, or help understand rapid solidification in other materials.

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