bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Dobbs v. Jackson Women’s Health Organization on Female Sterilization Rates at a Texas Military Medical Center, a Retrospective Cohort Study
Authors: Gottula Jessica L , Downey Abigail G , Shah Shenika P , Munisteri-Duff Meghan K , Keyser Erin A
Published: January 2025

Objective

Female sterilization is a common form of contraception in the United States. On June 24, 2022, the United States Supreme Court eliminated the federal standard protecting a woman’s right to abortion via Dobbs v. Jackson Women’s Health Organization. Since that time, there have been anecdotal increases in sterilization requests across the country, although there are no publications demonstrating this change. This study hypothesized that there would be increased female sterilization rates at a Texas military hospital post-Dobbs decision due to state restrictions as compared with a Washington military hospital.

Methods

This study retrospectively reviewed female sterilization rates from March 2022 to April 2023. The average rate of sterilization procedures performed pre-Dobbs decision was compared to the average rate following the Dobbs decision in a Texas and Washington military facility due to different state restrictions. The rates of sterilization were also stratified among demographic groups at the Texas military facility.

Results

Female sterilizations encompassed 24/230 (10.4%) of the gynecologic surgeries performed pre-Dobbs compared to 110/629 (17.5%) cases performed post-Dobbs (P = .01) in Texas. However, sterilization rates in Washington state remained the same, with 15/80 (18.7%) benign gynecologic surgeries pre-Dobbs and 28/185 (15.1%) post-Dobbs (P = .59). The average age of sterilization pre-Dobbs was 35 years compared to 33 years post-Dobbs (P = .04). Post-Dobbs group was less likely to use a barrier method prior to sterilization (P = 0.01).

Conclusion

The reproductive health of military medical beneficiaries at one military hospital was significantly impacted by the Dobbs v. Jackson Women’s Health Organization decision. Rates of female sterilization increased significantly. In addition, patients choosing permanent sterilization were younger and were less likely to use alternative, reversible contraceptive methods prior to surgery. This study demonstrates a significant change in contraceptive choices toward methods that incur greater surgical risks and potential for regret, as well as greater financial costs to the military health system.
Re-analysis of the anthropogenic effect of the COVID-19 global lockdown on nighttime lunar surface temperatures
Authors: Schonberg W , Haque S
Published: January 2025

A study by Durga Prasad and Ambily (2024) observed an anomalous decrease in the lunar surface temperatures during the period April-May 2020, which they then attributed to the anthropogenic effects of the COVID-19 global lockdown effect. We have re-examined their data and while the anomalous decrease in the lunar surface temperature during April- May 2020 appears in our analysis as well, so does another significant dip in early 2018. Furthermore, the decline to the minimum observed during April-May 2020 is seen to begin in 2019, that is, quite some time before the COVID-19 event that led to the global lockdown and the suggested anthropogenic effect of reduced pollution. We, therefore, conclude that one cannot attribute the effects of the observed changes in the lunar surface temperature during April-May 2020 directly and unambiguously to reduced human activity during the COVD-19 lockdown as claimed by Durga Prasad and Ambily (2024).
Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria
Authors: Mortensen Sofia , Kuncová Stanislava , Lormand Justin D , Myers Tanner M , Kim Soo-Kyoung , Lee Vincent T , Winkler Wade C , Sondermann Holger
Published: January 2025

Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner. Crystal structures of enzyme-substrate complexes reveal that specificity for DNA stems from a combination of conserved structural elements that exclude diribonucleotides as substrates. Consistently, diDNases fail to complement the loss of enzymes that act on diribonucleotides, indicating that these two groups of enzymes support distinct cellular functions. The genes encoding diDNases are found predominantly in genomic islands of Actinomycetes and Clostridia, which, together with their association with phage-defense systems, suggest potential roles in bacterial immunity.
One-pot ligation of multiple mRNA fragments on dsDNA splint advancing regional modification and translation
Authors: Xu Yunfan , Qi Shuopeng , Zhang Gongrui , Liu Dan , Xu Dejin , Qin Tong , Cheng Qin , Kang Han , Hu Bei , Huang Zhen
Published: January 2025

Region-specific RNA modifications are crucial for advancing RNA research and therapeutics, including messenger RNA (mRNA)-based vaccines and immunotherapy. However, the predominant method, synthesizing regionally modified mRNAs with short single-stranded DNA (ssDNA) splints, encounters challenges in ligating long mRNA fragments due to the formation of RNA self-folded complex structures. To address this issue, we developed an efficient strategy using an easily obtained long double-stranded DNA (dsDNA) as a ligation splint after in situ denaturing, while parts of this dsDNA are the templates for transcribing mRNA fragments. We observed that the denatured dsDNA formed a long hybrid duplex with these mRNA fragments, overcoming their structures. Further, our novel strategy remarkably facilitated the ligation of long mRNA fragments (especially structured ones), offering ligation efficiency up to 106-fold higher than the ssDNA method. Using this one-pot strategy, we conveniently synthesized the mRNAs with N1-methylpseudouridine (m1ψ) and 5-methylcytidine (m5C) modifications in specific regions. We have found that compared with the fully modified mRNAs, the 3′UTR m1ψ modifications alone increased the translation efficiency, and the combined modifications of the m1ψ-3′UTR and m5C-5′UTR/CDS exhibited higher translation efficiency and lower immunogenicity in general. Our study presents a broadly applicable strategy for producing regionally modified mRNAs, advancing the potential of mRNA therapeutics.
Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases
Authors: Jordano-Raya Marina , Schrader Carol E , Ariza Rafael R , Roldán-Arjona Teresa , Córdoba-Cañero Dolores
Published: January 2025

Apurinic/apyrimidinic (AP) endonucleases are key enzymes responsible for the repair of base-less nucleotides generated by spontaneous hydrolysis or as DNA repair intermediates. APE1, the major human AP endonuclease, is a druggable target in cancer and its biological function has been extensively studied. However, the molecular features responsible for its substrate specificity are poorly understood. We show here that, in contrast to APE1, its Arabidopsis ortholog ARP (apurinic endonuclease-redox protein) exhibits orphan base-dependent activity on double-stranded DNA and very poor AP cleavage capacity on single-stranded DNA (ssDNA). We found that these differences are largely a consequence of the variation at two DNA intercalating amino acids that have undergone divergent changes in the metazoan and plant lineages. Swapping the identity of the residue invading the minor groove is sufficient to switch the orphan base specificities of APE1 and ARP. The affinity for ssDNA is largely determined by the major groove invading residue, and swapping its identity switches the ability of APE1 and ARP to cleave AP sites in ssDNA. Importantly, we show that the critical residue for ssDNA cleavage is crucial for mammalian APE1 function in antibody class switch recombination, suggesting an evolutionary advantage for ssDNA activity. These findings provide new molecular insights into the evolution of AP endonucleases.
A Systematic Literature Review to Determine Gaps in Diagnosing Suspected Infection in Solid Organ Transplant Recipients
Authors: Park Sarah Y , Goldman Jason D , Levine Deborah J , Haidar Ghady
Published: January 2025

Background

Improved diagnostic testing (DT) of infections may optimize outcomes for solid organ transplant recipients (SOTR), but a comprehensive analysis is lacking.

Methods

We conducted a systematic literature review across multiple databases, including EMBASE and MEDLINE(R), of studies published between 1 January 2012–11 June 2022, to examine the evidence behind DT in SOTR. Eligibility criteria included the use of conventional diagnostic methods (culture, biomarkers, directed-polymerase chain reaction [PCR]) or advanced molecular diagnostics (broad-range PCR, metagenomics) to diagnose infections in hospitalized SOTR. Bias was assessed using tools such as the Cochrane Handbook and PRISMA 2020.

Results

Of 2362 studies, 72 were eligible and evaluated heterogeneous SOT populations, infections, biospecimens, DT, and outcomes. All studies exhibited bias, mainly in reporting quality. Median study sample size was 102 (range, 11–1307). Culture was the most common DT studied (N = 45 studies, 62.5%), with positive results in a median of 27.7% (range, 0%–88.3%). Biomarkers, PCR, and metagenomics were evaluated in 7, 19, and 3 studies, respectively; only 6 reported sensitivity, specificity, and positive/negative predictive values. Directed-PCR performed well for targeted pathogens, but only 1 study evaluated broad-range PCR. Metagenomics approaches detected numerous organisms but required clinical adjudication, with too few studies (N = 3) to draw conclusions. Turnaround time was shorter for PCR/metagenomics than conventional diagnostic methods (N = 4 studies, 5.6%). Only 6 studies reported the impact of DT on outcomes like antimicrobial use and length of stay.

Conclusions

We identified considerable evidence gaps in infection-related DT among SOT, particularly molecular DT, highlighting the need for further research.
Promoting Professionalism, Provoking Precarity: Security Assistance and the Risk of Military Coups
Authors: Darnton Christopher
Published: January 2025

When does foreign military assistance actually protect recipient governments, and when does it catalyze coups against them? In Adam Casey's Up in Arms: How Military Aid Stabilizes—and Destabilizes—Foreign Autocrats, great powers come preloaded with military models from their own history. These have different political risk profiles when exported, and the U.S. template of apolitical professionalism is particularly dangerous. This article reviews Up in Arms’ arguments about the sources and consequences of civil-military relationships, comparative Cold War case studies on the track record of security assistance and political regime durability, and contemporary policy lessons for military aid and alliances in an era of great power competition. It contextualizes these findings with the broader security assistance literature's mixed empirical results regarding democracy, human rights, and defense capability in recipient countries, and with scholars’ increasing emphasis, across research methods, on military training and education. In critiquing scope and methods both for the book and the field, the article calls for more case study work on democratic and counterinsurgent successes; closer analysis of military documents; and more systematic institutional disaggregation and ideational process tracing to assess the channels and conditions for effective security assistance.
Nutraceutical and low energy shockwave treatments improved sexual function recovery in a rat pelvic neurovascular injury model
Authors: Crisostomo-Wynne Theodore C , Hertz Alexandria M , Ferrini Monica G , Brand Timothy C , Salgar Shashikumar K
Published: January 2025

Background

Pelvic trauma can have long-lasting debilitating effects, including severe erectile dysfunction (ED) in men. While there are effective treatments for ED, these treat the symptoms not the cause. Those who suffer from an acute traumatic injury to the neurovascular supply of penis, may benefit from regenerative therapy. COMP4 is an all-natural herbal compound (Muira puama, Paullinia cupana, Ginger, and L-Citrulline) has potential to enhance penile vascular/smooth muscle/neuronal regeneration via Nitric Oxide synthesis. Low energy shockwave (LESW) therapy promotes nerve regeneration/angiogenesis by activating stem/progenitor cells.

Aim

To investigate the effects of the COMP4 and LESW for the treatment of ED in a rat pelvic trauma model.

Methods

The experimental design included five groups (Lewis rats aged 10-12 weeks; n = 8/group): (1) Sham, (2) Injury control, (3) Peanut Butter (PNB; Vehicle) Control, (4) COMP4, and (5) COMP4 + LESW. Pelvic neurovascular injury (PNVI) was induced by performing bilateral cavernous nerve crush injury and internal pudendal bundle ligation under general anesthesia. One week after PNVI rats received COMP4 (45 mg/kg b.wt./day) orally via PNB and/or LESW (1000 pulses at 0.06 mJ/mm2, 3 Hz, three times per week to the pelvis around penis) for 6 weeks. After 1 week of washout period, erectile function (EF) was assessed via intracavernous pressure (ICP; mmHg) measurements; rats euthanized, penile tissues collected for analyses.

Outcomes

COMP4 and LESW treatments improved EF recovery.

Results

There was a significant (P < .01) improvement in EF (ICP) with COMP4 (153.6 ± 26.6) and COMP4 + LESW (174.1 ± 38.2) treatments compared to vehicle (PNB) control (109.4 ± 32.6). COMP4 + LESW treatment enhanced EF compared to COMP4 alone. The base level ICP before treatments (Group 2) was 117.3 ± 6 and was lower (P < .01) than sham (165 ± 43.8) and COMP4 & COMP4 + LESW treated rats. Masson’s trichrome staining of corpus cavernosum penis demonstrated reduced (P < .001) smooth muscle-to-collagen (SM:C) ratio in injury and PNB controls compared to sham. COMP4 treatment following PNVI showed an increase (P < .05) in SM:C ratio. Adding LESW and COMP4 enhanced (P < .01) the SM:C ratio, suggesting a reduction in fibrosis. Western blot analysis revealed a significant increase in Endothelial Nitric Oxide Synthase and α-Smooth Muscle Actin (α-SMA) in the corpus cavernosum with COMP4 and COMP4 + LESW treatments compared to PNB control.

Clinical Implications

COMP4 and/or LESW can serve as an adjunct therapy to mitigate ED.

Strengths and Limitations

Identified novel treatment option to improve EF recovery. Unable to address in-depth cellular/molecular mechanisms.

Conclusions

COMP4 and LESW treatments appear to be promising to improve clinical EF recovery in pelvic trauma.
Customizing Tacrolimus Dosing in Kidney Transplantation: Focus on Pharmacogenetics
Authors: Lloberas Nuria , Vidal-Alabró Anna , Colom Helena
Published: January 2025

Different polymorphisms in genes encoding metabolizing enzymes and drug transporters have been associated with tacrolimus pharmacokinetics. In particular, studies on CYP3A4 and CYP3A5, and their combined cluster have demonstrated their significance in adjusting tacrolimus dosing to minimize under- and overexposure thereby increasing the proportion of patients who achieve tacrolimus therapeutic target. Many factors influence the pharmacokinetics of tacrolimus, contributing to inter-patient variability affecting individual dosing requirements. On the other hand, the growing use of population pharmacokinetic models in solid organ transplantation, including different tacrolimus formulations, has facilitated the integration of pharmacogenetic data and other variables into algorithms to easier implement the personalized dose adjustment in transplant centers. The future of personalized medicine in transplantation lies in implementing these models in clinical practice, with pharmacogenetics as a key factor to account for the high inter-patient variability in tacrolimus exposure. To date, three clinical trials have validated the clinical application of these approaches. The aim of this review is to provide an overview of the current studies regarding the different population pharmacokinetic including pharmacogenetics and those translated to the clinical practice for individualizing tacrolimus dose adjustment in kidney transplantation.
Outcomes of Tongue Reduction Surgery in Beckwith-Wiedemann Syndrome: A Systematic Review
Authors: Abraha Beraki , MacIntyre Olivia , Brennan Hannah , Hong Paul , Bezuhly Michael
Published: January 2025

Introduction:

Macroglossia is a frequent clinical feature of Beckwith-Wiedemann syndrome (BWS), a congenital overgrowth disorder. Macroglossia can lead to abnormal breathing, feeding, speech, and dentoskeletal development. Partial glossectomy is a common intervention aimed at reducing these abnormalities. The optimal timing of partial glossectomy remains controversial due to the potential need for secondary surgery and the ongoing growth of the tongue in early childhood.

Materials and Methods:

After PRISMA-ScR and PRISMA-S reporting standards, this systematic review included English language studies of patients with BWS who underwent partial glossectomy. Data were extracted, including patient age, clinical outcomes, and follow-up. Study evidence levels were categorized based on a recognized hierarchy, and bias was assessed using the MINORS criteria.

Results:

Early tongue reduction surgery (<24 mo) was associated with a lower incidence of class 3 occlusion and anterior open bite compared with later surgery. Improvements in speech intelligibility, tongue mobility, and breathing outcomes, including a reduction in obstructive sleep apnea, were observed, especially in early surgical groups. Feeding and drooling outcomes improved across both early and late surgical interventions, although no direct comparisons were made between the 2. Overall, tongue reduction surgery demonstrated benefits in functional outcomes, whereas dentoskeletal improvements remained variable.

Conclusion:

Although there is a lack of consensus to the optimal age for the procedure, overall tongue reduction surgery in BWS seems to have functional benefits, including in speech, feeding, and breathing. Dentoskeletal outcomes are more variable. Variability in macroglossia severity, surgical technique, and surgeon experience may account for differences in reported outcomes across studies.
Chronic Lymphocytic Inflammation With Pontine Perivascular Enhancement Responsive to Steroids Presenting With Predominantly Neuro-Ophthalmic Features
Authors: McDonald Heather M. , Handzic Armin , Mandell Daniel M. , Donaldson Laura , Trobe Jonathan D. , Margolin Edward
Published: January 2025

Background:

Chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS) is a rare and poorly understood inflammatory disorder of the central nervous system centered on the pons. It has a characteristic imaging appearance with enhancing and T2-hyperintense punctate and curvilinear lesions in the pons. The lesions lack restricted diffusion and have relatively little perilesional edema. Although patients typically present with gait ataxia and other sequelae of brainstem inflammation including diplopia, there is scant literature focusing on patients who present with primarily neuro-ophthalmic manifestations.

Methods:

Case series of 3 patients presenting with diplopia who had a final diagnosis of CLIPPERS.

Results:

Case descriptions of a 71-year-old man, 61-year-old woman, and 38-year-old man are reported. Diplopia was the chief presenting complaint, owing to internuclear ophthalmoplegia, sixth nerve palsy, or skew deviation. All patients had nystagmus and gait ataxia. Brain MRI displayed punctate or curvilinear enhancement of pontine/middle cerebellar peduncle lesions without restricted diffusion. All patients achieved rapid improvement after corticosteroid treatment.

Conclusions:

In 3 patients with CLIPPERS, the main presenting complaint was diplopia. The distinctive imaging signs led to a strong presumption of CLIPPERS, permitting a truncated evaluation and early corticosteroid treatment, which provided rapid reversal of clinical and imaging manifestations.
Ventricular tachycardia unveiling severe undiagnosed hypothyroidism
Authors: Waddankeri Swaraj S. , Kohir Goutami V. , Bijapur Karan J. , Yelsangikar Goutam R. , Patil Veeresh
Published: January 2025

Hypothyroidism is typically associated with bradyarrhythmias, but can rarely precipitate life-threatening ventricular arrhythmias. We present a case of severe hypothyroidism manifesting as polymorphic ventricular tachycardia (VT). A previously healthy woman in her early 50s presented with an acute onset of breathlessness and on examination had hypotension and tachycardia. ECG revealed polymorphic VT, promptly terminated by defibrillation using 200J biphasic shock. Investigations uncovered severe primary hypothyroidism (thyroid-stimulating hormone: 142 mIU/l) and left ventricular (LV) dysfunction with ejection fraction (EF) of 35%. Coronary angiogram was normal. Treatment with levothyroxine and standard heart failure therapy was initiated. In conclusion, at 3- and 6-month follow-ups, the patient remained asymptomatic and had no episodes of tachyarrhythmias without antiarrhythmic drugs, and her LV function normalized (EF: 55%). This case highlights the importance of considering hypothyroidism in patients presenting with unexplained ventricular arrhythmias.
Ultrasensitive turn-off fluorescent sensor for estimation of the new influenza antiviral prodrug baloxavir marboxil in its pharmaceutical formulation
Authors: Gouda Amira S. , Rezk Mamdouh R. , Abdel-Megied Ahmed M. , Marzouk Hoda M.
Published: January 2025

Carbon quantum dots (CQDs) are a recently developed class of fluorescent nanoparticles made from carbon. Co-doping with heteroatoms such as nitrogen and sulfur improved the properties and generated a high quantum yield. In the proposed study, we utilized a simple, cost-effective, single-stage hydrothermal approach to produce extreme photoluminescence co-doped, nitrogen and sulfur, CQDs (N,S-CODs). Thiosemicarbazide was used as a nitrogen and sulfur source, while citric acid was used as a carbon source to produce fluorescent probes. The prepared N,S-CQDs were subjected to extensive characterization. The generated N,S-CQDs yielded strong fluorescence emission at
λ
em
430.0 nm after excitation at
λ
ex
360.0 nm, with a relatively high quantum yield of 41.3% utilizing quinine sulfate as a reference fluorescent compound. These N,S-CQDs were applied as fluorescent nanosensors for the ultrasensitive spectrofluorimetric determination of baloxavir marboxil (BXM) directly without pre-derivatization for the first time. BXM effectively quenches the native fluorescence of N,S-CQDs. Considering the optimal conditions, the fluorescence intensity reduction of N,S-CQDs exhibited a ‘turn-off’ response to BXM at concentrations of 10.0–100.0 ng ml
−1
, with detection limits of 1.88 ng ml
−1
and quantitation limits of 5.69 ng ml
−1
, respectively. The proposed method determined BXM successfully in its tablet dosage form and further expanded to confirm the content uniformity of the tablet units in agreement with USP guidelines.
Rural Diets Under Pressure: Food Environments and their Influence on Food Choice in South Asia
Authors: Chauhan Alka , Scott Samuel , Joe William , Maharjan Nanda Kumar , Menon Purnima ,   TAFSSA collaborators, Chakrabarti Suman
Published: January 2025

The rapid South Asia rural transformation, driven by globalization and industrialization, has introduced a complex interaction between traditional and modern food systems. This study characterizes rural food environments in five districts across Bangladesh, India, and Nepal, focusing on how affordability, availability, accessibility, desirability, and convenience shape dietary choices and quality. Through extensive household and market surveys, we find rural diets characterized by low intake of healthy foods and moderate to high consumption of unhealthy options, influenced by a lack of affordability and the desirability and widespread availability of cheap ultra-processed products in rural markets. Snacking plays a significant role in shaping dietary patterns, promoting both dietary diversity and unhealthy food consumption. These findings provide essential insights for designing interventions tailored to rural food systems, supporting efforts to improve nutrition and health outcomes in rapidly changing markets.
Targeting and combating drug resistance in triple-negative breast cancer using nano polymer: Efficacy of A6 peptide-PLGA-PEG nanoparticle loaded with doxorubicin and anti-miR-21 inin vitroandvivo model
Authors: Ibrahim Zaidah , Chong Pei Pei , Al-Moustafa Hasan , Abdullah Maizaton Atmadini , Chik Zamri
Published: January 2025

Triple-negative breast cancer (TNBC) poses a significant challenge in treatment due to the emergence of drug resistance to standard chemotherapeutics, along with associated risks to non-targeted tissues. This study is dedicated to developing a nanoparticle drug delivery system utilizing PLGA-PEG nanoparticles (NP) with the integration of A6 peptide (NPA6) as a specific targeting ligand for TNBC. Encapsulating Doxorubicin (DOX) and antisense-miR-21 (AM21), these nanoparticles are designed to counter drug resistance in vitro and in vivo. Characterized by an average size of 103.5 (±8.1) nm and remarkable DOX encapsulation efficiency, these nanoparticles have been successfully engineered. Results demonstrate that NPA6.DOX.AM21 effectively mitigates drug resistance, displaying a significantly decreased doxorubicin IC50as opposed to free DOX (2.5 µM vs 25.7µMrespectively, p<0.01). In mice models, the A6 peptide-incorporated formulation (NPA6.DOX, NPA6.DOX.AM21) exhibits substantial tumour size reduction and increased doxorubicin concentration within tumours, all while minimizing non-specific doxorubicin exposure compared to non-A6 formulations (NPDOX, FREE DOX) treatments. This innovative PLGA-PEG-A6 peptide complex loaded with DOX and AM21 showcases superior efficacy in surmounting cell resistance in breast cancer cell line, targeting tumour progression, and decreasing drug distribution in non-targeted organs in mice. These results hold promise for enhanced combat against drug resistance and precise chemotherapy, hence potentially improving patient outcomes and survival rates.

Graphical abstact

Figure Graphical abstract of the study. Fron left to right, development of nanoparticles formulation a followed by characterization and efficacy of the nanoparticle formulation inin vitroandin vivoto reduce drug resistance and target triple negative breast cancer (TNBC). PLGA: polylactic-co-glycolic acid, PEG: polyethylene glycol, A6: A6 peptide, DOX: Doxorubicin, AM21: antisense-microRNA -21

Highlights

The nanoparticle of A6 conjugated PLGA-PEG co-loaded Doxorubicin with anti-miRNA21 (NPA6.DOX.AM21) was successfully fabricated with the size of 99.8 - 103.5 nm diameter and PDI 0.2 with high drugs encapsulation efficiency.

NPA6.DOX.AM21 increased cell death, reduced drug resistance in MDA MB-231 resistant cells, and reduced IC50of doxorubicin dose.

NPA6.DOX.AM21 targeted and reduced TNBC tumour size, with high doxorubicin distribution in tumor and less accumulation in off-target organs, in comparison to the control in mice model.
Structural basis for postfusion-specific binding to Respiratory Syncytial Virus F protein by the canonical antigenic site I antibody 131-2a
Authors: Peng Weiwei , Šiborová Marta , Wu Xuesheng , Du Wenjuan , Schulte Douwe , Pronker Matti F. , de Haan Cornelis A. M. , Snijder Joost
Published: January 2025

The Respiratory Syncytial Virus (RSV) Fusion (F) protein is a major target of antiviral antibodies following natural infection or vaccination and responsible for mediating fusion between the viral envelope and the host membrane. The fusion process is driven by a large-scale conformational change in F, switching irreversibly from the metastable prefusion state to the stable postfusion conformation. Previous research has identified six distinct antigenic sites in RSV-F, termed sites Ø, I, II, III, IV, and V. Of these, only antigenic site I is fully specific to the postfusion conformation of F. A monoclonal antibody 131-2a that specifically targets postfusion F has been widely used as a research tool to probe for postfusion F and to define antigenic site I in serological studies, yet its sequence and precise epitope have remained unknown. Here we use mass spectrometry-basedde novosequencing of 131-2a to reverse engineer a recombinant product and study the epitope to define antigenic site I with molecular detail, revealing the structural basis for the antibody’s specificity towards postfusion RSV-F.
C-di-GMP is Required for Swarming inE. coli: a Role for DgcO and Colanic Acid
Authors: Hwang YuneSahng , Perez Marta , Holzel Rebecca , Harshey Rasika M.
Published: January 2025

Many bacteria use flagella to swim individually through bulk liquid, or swarm collectively over a semi-solid surface. InE. coli, c-di-GMP inhibits swimming via the effector protein YcgR. We show in this study that contrary to its effect on swimming, a certain threshold level of c-di-GMP is required for swarming. Gene expression profiles first indicated that several c-di-GMP synthases –dgcJ, dgcM, dgcO- were upregulated during swarming. Of these, we found DgcO to play a critical role. DgcO is reported to affect PGA (poly-β-1,6-N-acetylglucosamine) synthesis inE. coli. We show that DgcO also promotes production of colanic acid - one of the three major exopolysaccharides inE. coli, and that colanic acid has hitherto-unknown surfactant properties that are expected to aid swarming.

Importance

It is well-established that in bacteria, c-di-GMP inhibits flagella-driven motility at various points in the pathway. Concomitantly, elevated c-di-GMP levels induce the expression and synthesis of a variety of exopolysaccharides that enmesh the bacteria in a biofilm, thereby also interfering with flagella function. This study reports the surprising finding that inE. coli, the exopolysaccharide colanic acid is required to enable surface navigation and that the diguanylate cyclase DgcO is employed for this purpose. For surface navigation, there appears to be a sweet spot where c-di-GMP levels are just right to produce polysaccharides that can serve as surfactants and wetting agents rather than promote formation of biofilms.
Checkpoint receptors in circulating γδ T cells can discern the outcome of cancer immunotherapy
Authors: Catafal Tardos Elisa , Dachicourt Lola , Baglioni Maria Virginia , Fares da Silva Marcelo Gregorio Filho , Secci Davide , Donia Marco , Kverneland Anders , Svane Inge Marie , Bekiaris Vasileios
Published: January 2025

Gamma delta (γδ) T cells are innate-like lymphocytes that in humans can be broadly classified into two main subtypes based on their unique TCRδ chain, Vδ1 and Vδ2. Both subsets have potent anti-tumor properties and the presence of Vδ1 cells in the tumor is often associated with positive prognosis. Herein, we investigated the molecular interplay between immune checkpoint receptors (ICRs), IC blockade (ICB) therapy and γδ T cells. We show that ICRs display differential expression and regulation by the JAK-STAT pathway in circulating Vδ1 and Vδ2 cells and identify constitutive (e.g. TIGIT, PD-1) and inducible (e.g. TIM-3, LAG-3, CTLA-4) ICRs. In melanoma, Vδ1 cells, especially in patients who did not respond to ICB or required combination therapy, expressed high levels of ICR, TOX and inhibitory killer Ig-like receptors (KIR) transcripts, reminiscent of an exhaustion transcriptional signature. At the same time all γδ T cells had a prominent downregulation in AP-1 transcription factors. Patient derived cells were functionally competent, although induction of LAG-3 and CTLA-4 was impaired. In the context of anti-PD-1 monotherapy, Vδ1 cells specifically bound high levels of therapeutic antibody but only in patients who responded to treatment, revealing a potential new prognostic marker for evaluating the efficacy of ICB therapy. Finally, expression of KIR genes in Vδ1 cells was downregulated in response to successful ICB therapy. Collectively, our data indicate an intricate relationship between ICRs, putatively also KIRs, and γδ T cells and reveal novel approaches by which these cells can be harnessed in order to discern or improve cancer immunotherapy.
ANGPTL3 binds to PCSK9 to coordinately regulate intracellular lipid homeostasis
Authors: Bini Simone , Pecce Valeria , Grimaldos Alessandra Pinzon , Di Costanzo Alessia , Minicocci Ilenia , Covino Stella , Tramontano Daniele , Piconese Silvia , D’Erasmo Laura , Arca Marcello
Published: January 2025

ANGPTL3 and PCSK9 are core proteins involved in lipid metabolism. Literature evidence highlights a potential mutual regulation between them: patients harboring loss-of-function variants in ANGPTL3 show reduced levels of circulating PCSK9. After predicting their interaction using an in-silico model, we verified the direct interaction between ANGPTL3 and PCSK9 through co-immunoprecipitation. The ANGPTL3-PCSK9 complex persisted underfastingconditions and dissociated underfeedingconditions. Treatment with human LDLs was sufficient to simulate the feeding response. Then, we observed that the overexpression of PCSK9 enhances the uptake of LDLs that are not further metabolized, while the overexpression of ANGPTL3 enhances LDL turnover. The overexpression of both proteins restored LDL uptake and degradation, which became comparable to those of control cells. In conclusion, our findings indicate the existence of an ANGPTL3-PCSK9 complex, which coordinately contributes to the regulation of intracellular lipid homeostasis, aiming to prevent cellular metabolic overload.

GRAPHICAL ABSTRACT

Graphical abstract

Mechanistic model of ANGPTL3-PCSK9 complex function in the regulation of lipoprotein metabolism

Increased uptake of extracellular nutrients determines the separation of the ANGPTL3-PCSK9 complex. The two free proteins have different functions (1). Increased levels of PCSK9 determine an increased intracellular entrapment of circulating LDLs (2) that are not catabolized unless there is a presence of high intracellular levels of ANGPTL3. Increased ANGPTL3 levels also favor ApoB lipidation and secretion (3), whereas an increase in intracellular PCSK9 increases intracellular ApoB degradation. The increase in intracellular PCSK9 also determines a block in lipogenesis and favors beta-oxidation, thus decreasing the intracellular lipid content (4).
Maternal immune activation imprints a regulatory T cell deficiency in offspring that drives an autism-like phenotype
Authors: Ellul Pierre , Fourcade Gwladys , Mhanna Vanessa , Coatnoan Nicolas , Bodula Susana , Seilhean Danielle , Mouton Laura , Marguerit Gwendolyn , Delorme Richard , Mi Tian , Youngblood Ben , Rosenzwajg Michelle , Tchitchek Nicolas , Klatzmann David
Published: January 2025

Maternal immune activation (MIA) triggers an IL-17-driven autism spectrum disorder (ASD) in mouse and human offspring. While regulatory T cells (Tregs) regulate Th17 cells, their involvement in MIA and ASD pathogenesis is unknown. At the maternal level, we show that Treg stimulation suppresses interleukin-17 (IL-17) production and prevents ASD-like behaviors in offspring. At the offspring level, we show that MIA imprints a systemic and brain Treg deficiency, as evidenced by alterations in the methylome, transcriptome, and functional assays. This deficiency promotes brain inflammation, characterized by infiltration of IL-17–producing cells and neutrophils into the meninges and alterations in cortical brain structure. Stimulation of offspring Tregs with interleukin-2 reversed brain inflammation and cured established ASD-like behaviors. Thus, MIA-induced ASD is a neuroimmune disorder that can be reversed by immunomodulation.

One sentence abstract

Maternal immune activation during pregnancy imprints a Treg deficiency in offspring that perpetuates brain inflammation and an autism-like phenotype, which can be reversed by Treg stimulation.
Immunogenicity of Rabies Virus G-Protein mRNA Formulated with Muscle Targeting Lipid Nanoparticles in Mice
Authors: Li Qin , Bai Huarong , Yu Xueliang , Liu Qiang , Hu Rongkuan
Published: January 2025

Rabies is a preventable zoonotic disease caused by the rabies virus (RABV) with a high mortality rate. Most vaccines on the market or under development have issues such as a low single-dose neutralization titer, complex processes, and high costs. During the COVID-19 pandemic, the successful development of mRNA vaccines has opened up a new avenue for preventive vaccines. As a new technology, mRNA has higher scalability. In this study, we designed an mRNA encoding the RV-G protein, encapsulated by our own muscle targeting lipid nanoparticles (LNP), and evaluated the expression of the RV-G protein in vitro, its immunogenicity, and its protection against virus infection in vivo. The results showed that RV-G mRNA was significantly expressed in vitro. High Virus-IgG binding titers and Virus-neutralizing antibody titers (VNT) were induced by immunization with RV-G mRNA-LNP. Additionally, our results show that the RV-G mRNA vaccine is better than commercially available vaccines in mice.
Deep Learning for Biomarker Discovery in Cancer Genomes
Authors: Unger Michaela , Loeffler Chiara M. L. , Žigutytė Laura , Sainath Srividhya , Lenz Tim , Vibert Julien , Mock Andreas , Fröhling Stefan , Graham Trevor A. , Carrero Zunamys I. , Kather Jakob Nikolas
Published: January 2025

Background

Genomic data is essential for clinical decision-making in precision oncology. Bioinformatic algorithms are widely used to analyze next-generation sequencing (NGS) data, but they face two major challenges. First, these pipelines are highly complex, involving multiple steps and the integration of various tools. Second, they generate features that are human-interpretable but often result in information loss by focusing only on predefined genetic properties. This limitation restricts the full potential of NGS data in biomarker extraction and slows the discovery of new biomarkers in precision oncology.

Methods

We propose an end-to-end deep learning (DL) approach for analyzing NGS data. Specifically, we developed a multiple instance learning DL framework that integrates somatic mutation sequences to predict two compound biomarkers: microsatellite instability (MSI) and homologous recombination deficiency (HRD). To achieve this, we utilized data from 3,184 cancer patients obtained from two public databases: The Cancer Genome Atlas (TCGA) and the Clinical Proteome Tumor Analysis Consortium (CPTAC).

Results

Our proposed deep learning method demonstrated high accuracy in identifying clinically relevant biomarkers. For predicting MSI status, the model achieved an accuracy of 0.98, a sensitivity of 0.95, and a specificity of 1.00 on an external validation cohort. For predicting HRD status, the model achieved an accuracy of 0.80, a sensitivity of 0.75, and a specificity of 0.86. Furthermore, the deep learning approach significantly outperformed traditional machine learning methods in both tasks (MSI accuracy, p-value = 5.11×10−18; HRD accuracy, p-value = 1.07×10−10). Using explainability techniques, we demonstrated that the model’s predictions are based on biologically meaningful features, aligning with key DNA damage repair mutation signatures.

Conclusion

We demonstrate that deep learning can identify patterns in unfiltered somatic mutations without the need for manual feature extraction. This approach enhances the detection of actionable targets and paves the way for developing NGS-based biomarkers using minimally processed data.
EASYstrata: a new workflow to infer evolutionary strata along sex chromosomes and other supergenes
Authors: Rougemont Quentin , Lucotte Elise , Boyer Loreleï , Jalaber Alexandra , Snirc Alodie , Giraud Tatiana , Rodríguez de la Vega Ricardo C.
Published: January 2025

New reference genomes and transcriptomes are becoming increasingly available across the whole tree of life, opening new avenues to tackle exciting evolutionary questions. However, there are still challenges associated with annotating genomes, aligning sequences, inferring evolutionary processes and a lack of methodological standardisation. Here, we propose a new workflow designed for evolutionary analyses to overcome these challenges, facilitating the detection of recombination suppression and its consequences in terms of rearrangements and transposable element accumulation. To do so, we assemble multiple bioinformatic steps in a single, reproducible and easy-to-use workflow. We combine state-of-the-art tools to quickly detect transposable elements, annotate newly assembled genomes, infer gene orthology relationships, compute divergence between sequences, infer evolutionary strata (i.e. stepwise extension of recombination suppression) and their structural rearrangements, and visualise the results at different steps in the process. This workflow was called EASYstrata and was applied to reannotate a set of 42 published genomes fromMicrobotryumfungi. We show in case examples that we recover the same strata as previously described. While this tool was mostly developed with the goal to infer divergence between sex or mating-type chromosomes, it can be applied to any pair of haplotypes whose pattern of divergence might be of interest, e.g. supergenes in autosomes. This workflow will facilitate the study of the numerous non-model species for which newly sequenced phased diploid genomes are becoming available.
Behavioral and neural sound classification: Insights from natural and synthetic sounds
Authors: Ogg Mattson
Published: January 2025

Throughout the course of a day, human listeners encounter an immense variety of sounds in their environment. These are quickly transformed into mental representations of objects and events that guide subsequent cognition and behavior in the world. Previous studies using behavioral and temporally resolved neuroimaging methods have demonstrated the importance of certain acoustic qualities for distinguishing among different classes of sounds during the early time period following sound onset (noisiness, spectral envelope, spectrotemporal change over time, and change in fundamental frequency over time). However, this evidence is largely based on correlational studies of natural sounds. Thus, two additional behavioral (Experiment 1) and EEG (Experiment 2) studies further tested these results using a set of synthesized stimuli (interspersed among a new set of natural sounds) that explicitly manipulated previously identified acoustic dimensions. In addition to finding similar correlational results as previous work (using new natural stimuli and tasks), classification results for the synthesized acoustic feature manipulations reinforced the importance of aperiodicity, spectral envelope, spectral variability and fundamental frequency change for representations of superordinate sound-categories. Analyses of the synthesized stimuli suggest that aperiodicity is a particularly robust cue in distinguishing some categories and that speech is difficult to characterize within this framework (i.e., using these acoustic dimensions and synthetic feature manipulations). These results provide a deeper understanding of the neural and perceptual dynamics that support the recognition of behaviorally important categories of sound in the time windows soon after sound onset.
Hybrid supramolecular-covalent bioresin promotes cell migration and self-assembly in light-based volumetric bioprinted constructs
Authors: Falandt Marc , Bernal Paulina Nunez , Longoni Alessia , Buchholz Maj-Britt , Quilis Pere Català , Widmann Klement , Barrera-Roman Mario , Malda Jos , Vermonden Tina , Rios Anne , Levato Riccardo
Published: January 2025

There is an increasing need for novel biomaterials compatible with advanced biofabrication technologies, which also permit cells to remodel their microenvironment. This remodelling is crucial for maturing tissue constructs into fully functional tissue replacements. Recent progress in supramolecular chemistries has allowed for the production of dynamic biomaterials. Their properties enable bonds to be reversibly broken by cells, facilitating processes requiring morphological changes or migration, crucial for tissue development and homeostasis. Here, we present a one-of-its-kind gelatin-based hybrid covalent/supramolecular biomaterial. We demonstrate the advantage of adding supramolecular-reactive moieties on covalent materials, over covalent bonds alone, in facilitating processes such as cell growth, migration, spreading and organoid proliferation. This is exemplified by enhanced MSC and T cell migration and improved vascular network formation in hybrid hydrogels over covalent-only materials. The combination of supramolecular and covalent bonds further enabled control over photocrosslinking, allowing the use of the material in volumetric bioprinting of complex structures with high shape fidelity. As a proof-of-concept we bioprinted complex breast-like structures from encapsulated normal breast cell lines with a tumor organoid core. We demonstrated that engineered T cells can migrate large distances into the breast tissue, specifically targeting tumor cells.

Graphical abstract
Eye metrics are a marker of visual conscious awareness and neural processing in cerebral blindness
Authors: Kronemer Sharif I. , Gobo Victoria E. , Japee Shruti , Merriam Eli , Osborne Benjamin , Bandettini Peter A. , Liu Tina
Published: January 2025

Damage to the primary visual pathway can cause vision loss. Some cerebrally blind people retain degraded vision or sensations and can perform visually guided behaviors. These cases motivate investigation and debate on blind field conscious awareness and linked residual neural processing. A key challenge in this research is that subjective measures of blind field visual conscious awareness can be misleading. Alternatively, eye metrics, including pupil size and eye movements are promising objective markers of conscious awareness and brain activity. In this study, we examined stimulus-evoked changes in pupil size, blinking, and microsaccades in the sighted and blind field of cerebrally blind participants. Using standard analysis and innovative machine learning methods, our findings support that eye metrics can infer blind field conscious awareness, even when behavioral performance on a visual perception task indicated otherwise. Furthermore, these eye metrics were linked to blind field visual stimulus-evoked occipital cortical field potentials. These findings support recording eye metrics in cerebral blindness and highlight potential clinical applications, including tracking the recovery of conscious vision and visual neural processing.