A survey of k-mer methods and applications in bioinformatics.

The rapid progression of genomics and proteomics has been driven by the advent of advanced sequencing technologies, large, diverse, and readily available omics datasets, and the evolution of computational data processing capabilities. The vast amount of data generated by these advancements necessitates efficient algorithms to extract meaningful information. K-mers serve as a valuable tool when working with large sequencing datasets, offering several advantages in computational speed and memory efficiency and carrying the potential for intrinsic biological functionality. This review provides an overview of the methods, applications, and significance of k-mers in genomic and proteomic data analyses, as well as the utility of absent sequences, including nullomers and nullpeptides, in disease detection, vaccine development, therapeutics, and forensic science. Therefore, the review highlights the pivotal role of k-mers in addressing current genomic and proteomic problems and underscores their potential for future breakthroughs in research.

kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.

The decrease in sequencing expenses has facilitated the creation of reference genomes and proteomes for an expanding array of organisms. Nevertheless, no established repository that details organism-specific genomic and proteomic sequences of specific lengths, referred to as kmers, exists to our knowledge. In this article, we present kmerDB, a database accessible through an interactive web interface that provides kmer-based information from genomic and proteomic sequences in a systematic way. kmerDB currently contains 202,340,859,107 base pairs and 19,304,903,356 amino acids, spanning 54,039 and 21,865 reference genomes and proteomes, respectively, as well as 6,905,362 and 149,305,183 genomic and proteomic species-specific sequences, termed quasi-primes. Additionally, we provide access to 5,186,757 nucleic and 214,904,089 peptide sequences absent from every genome and proteome, termed primes. kmerDB features a user-friendly interface offering various search options and filters for easy parsing and searching. The service is available at: www.kmerdb.com.

Utilizing nullomers in cell-free RNA for early cancer detection.

Early detection of cancer can significantly improve patient outcomes; however, sensitive and highly specific biomarkers for cancer detection are currently missing. Nullomers are the shortest sequences that are absent from the human genome but can emerge due to somatic mutations in cancer. We examine over 10,000 whole exome sequencing matched tumor-normal samples to characterize nullomer emergence across exonic regions of the genome. We also identify nullomer emerging mutational hotspots within tumor genes. Finally, we provide evidence for the identification of nullomers in cell-free RNA from peripheral blood samples, enabling detection of multiple tumor types. We show multiple tumor classification models with an AUC greater than 0.9, including a hepatocellular carcinoma classifier with an AUC greater than 0.99.

Lithium Dendrite Propagation in Ta-Doped Li7La3Zr2O12 (LLZTO): Comparison of Reactively Sintered Pyrochlore-to-Garnet vs LLZTO by Solid-State Reaction and Conventional Sintering.

Ta-doped Li7La3Zr2O12 (LLZTO) garnet is a promising Li-ion-conducting ceramic electrolyte for solid-state batteries. However, it is still challenging to use LLZTO in Li metal batteries operating at high current densities because of the tendency for Li metal to nucleate and propagate along the grain boundaries. In this study, we carry out a detailed investigation to elucidate the effect of microstructure and grain size on the electrochemical properties and short circuit behavior in LLZTO. Pellets were prepared using reactive sintering from pyrochlore precursors (a method called pyrochlore-to-garnet, P2G) and compared with LLZTO synthesized using solid-state reaction (SSR) followed by conventional pressureless sintering. Both preparation methods were controlled to keep the phase and elemental composition, ionic and electronic conductivity, relative density, and area-specific resistance of the pellets constant. Reflection electron energy loss spectroscopy and X-ray photoelectron spectroscopy confirm that both types of LLZTO have similar band gaps and chemical states. Microstructure analysis shows that the P2G method results in LLZTO with an average grain size of around 3 µm, which is much smaller than the grain sizes (as large as 20 µm) seen in SSR LLZTO. Galvanostatic Li stripping/plating and linear sweep voltammetry measurements show that P2G LLZTO can withstand higher critical current densities (up to 0.4 mA/cm2 in bidirectional cycling and >1 mA/cm2 for unidirectional) than those seen in SSR LLZTO. Post-mortem examination reveals much less Li deposition along the grain boundaries of P2G LLZTO, particularly in the bulk of the pellet, compared to SSR LLZTO after cycling. The improved cycling behavior in P2G LLZTO despite the higher grain boundary area could be from more homogeneous current density at the interfaces and different grain boundary properties arising from the liquid-phase, reactive sintering method. These results suggest that the effect of grain size on Li dendrite propagation in LLZO may be highly dependent on the synthesis and sintering method employed.

Failure Modes of Flexible LiCoO2 Cathodes Incorporating Polyvinylidene Fluoride Binders with Different Molecular Weights.

Understanding the mechanical failure modes of lithium-ion battery [Li-ion batteries (LIBs)] electrodes is exceptionally important for enabling high specific energy and flexible LIB technologies. In this work, the failure modes of lithium cobalt oxide (LCO) cathodes under repeated bending and the role of the polymer binder in improving the mechanical durability of the LCO electrodes for use in flexible LIBs are investigated. Mechanical and electrochemical evaluations of LCO electrodes (areal capacity of ≥2.5 mA h cm-2) employing poly(vinylidene fluoride) (PVDF) binder were carried out, followed by extensive optical and electron microscopies. We find that the molecular weight (MW) of the PVDF significantly influenced the surface and bulk microstructure of the LCO electrodes, particularly the distribution of carbon additive and binder, which plays a crucial role in affecting the mechanical and electrochemical properties of the electrodes. Multiple mechanical failure modes (e.g., surface scratches and microcracks) observed in the LCO electrodes subjected to repeated bending originated from the use of low MW PVDF; these failure modes were successfully mitigated by using a high MW PVDF. Remarkably, the optimized flexible LCO electrode incorporating high MW PVDF showed comparable discharge capacity retention during galvanostatic cycling after repeated bending (7000 cycles at 50 mm bending diameter) to electrodes not subjected to the repeated bending. This study highlights the importance of carrying out a comprehensive investigation of the failure mechanisms in flexible electrodes, which identified the pivotal role of the PVDF MW in the electrode microstructure and its effects on the electrode resilience to failure during repeated bending.

Peptide absent sequences emerging in human cancers.

Early diagnosis of cancer can significantly improve survival of cancer patients; however sensitive and highly specific biomarkers for cancer detection are currently lacking for most cancer types. Nullpeptides are short peptides that are absent from the human proteome. Here, we examined the emergence of nullpeptides during cancer development. We analyzed 3,600,964 somatic mutations across 10,064 whole exome sequencing tumor samples spanning 32 cancer types. We analyze RNA-seq data from primary tumor samples to identify the subset of nullpeptides that emerge in highly expresed genes. We show that nullpeptides, and particularly the subset that is highly recurrent across cancer patients, can be identified in tumor biopsy samples. We find that cancer genes show an excess of nullpeptides and detect nullpeptide hotspots in specific loci of oncogenes and tumor suppressors. We also observe that recurrent nullpeptides are more likely to be found in neoantigens, which have been shown to be effective targets for immunotherapy, suggesting that they can be used to prioritize candidates. Our findings provide evidence for the utility of nullpeptides as cancer detection and therapeutic biomarkers.

Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.

Early detection of human disease is associated with improved clinical outcomes. However, many diseases are often detected at an advanced, symptomatic stage where patients are past efficacious treatment periods and can result in less favorable outcomes. Therefore, methods that can accurately detect human disease at a presymptomatic stage are urgently needed. Here, we introduce "frequentmers"; short sequences that are specific and recurrently observed in either patient or healthy control samples, but not in both. We showcase the utility of frequentmers for the detection of liver cirrhosis using metagenomic Next Generation Sequencing data from stool samples of patients and controls. We develop classification models for the detection of liver cirrhosis and achieve an AUC score of 0.91 using ten-fold cross-validation. A small subset of 200 frequentmers can achieve comparable results in detecting liver cirrhosis. Finally, we identify the microbial organisms in liver cirrhosis samples, which are associated with the most predictive frequentmer biomarkers.

Functional characterization of Alzheimer's disease genetic variants in microglia.

Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.

Self-supported polypyrrole flexible electrodes for electrochemical reduction of nitrite.

The efficiency of an electrochemical oxidation/reduction process strongly depends on the working electrode's surface area to volume ratio. By making electrodes flexible and employing different configurations such as roll-to-roll membrane, the surface area to volume ratio can be enhanced, therefore improving the overall efficiency of electrochemical processes. Conductive polymers emerge as a new framework to enable alternative electrochemical water treatment cell configurations. Self-standing polypyrrole flexible electrodes were synthesized by electropolymerization and evaluated on the treatment of an oxyanion pollutant: nitrite. Mechanical characterization through stress-strain curves and bending tests demonstrated high electrode resilience that sustained over 1000 bending cycles without impacting mechanical integrity or electrocatalytic responses. The electrocatalytic response towards nitrite reduction was assessed under linear scan voltammetry (LSV) and removal performance evaluated under potentiostatic conditions reaching 79% abatement of initial concentrations of nitrite of 15 mg/L [NO2--N]. Self-standing flexible electrodes appear as a novel framework to enable modular compact water treatment unit designs that maximize the electrode area/volume ratio and substitute expensive platinum group metal (PGMs) electrocatalysts.

Quasi-prime peptides: identification of the shortest peptide sequences unique to a species.

Determining the organisms present in a biosample has many important applications in agriculture, wildlife conservation, and healthcare. Here, we develop a universal fingerprint based on the identification of short peptides that are unique to a specific organism. We define quasi-prime peptides as sequences that are found in only one species, and we analyzed proteomes from 21 875 species, from viruses to humans, and annotated the smallest peptide kmer sequences that are unique to a species and absent from all other proteomes. We also perform simulations across all reference proteomes and observe a lower than expected number of peptide kmers across species and taxonomies, indicating an enrichment for nullpeptides, sequences absent from a proteome. For humans, we find that quasi-primes are found in genes enriched for specific gene ontology terms, including proteasome and ATP and GTP catalysis. We also provide a set of quasi-prime peptides for a number of human pathogens and model organisms and further showcase its utility via two case studies for Mycobacterium tuberculosis and Vibrio cholerae, where we identify quasi-prime peptides in two transmembrane and extracellular proteins with relevance for pathogen detection. Our catalog of quasi-prime peptides provides the smallest unit of information that is specific to a single organism at the protein level, providing a versatile tool for species identification.

Transcription factor binding site orientation and order are major drivers of gene regulatory activity.

The gene regulatory code and grammar remain largely unknown, precluding our ability to link phenotype to genotype in regulatory sequences. Here, using a massively parallel reporter assay (MPRA) of 209,440 sequences, we examine all possible pair and triplet combinations, permutations and orientations of eighteen liver-associated transcription factor binding sites (TFBS). We find that TFBS orientation and order have a major effect on gene regulatory activity. Corroborating these results with genomic analyses, we find clear human promoter TFBS orientation biases and similar TFBS orientation and order transcriptional effects in an MPRA that tested 164,307 liver candidate regulatory elements. Additionally, by adding TFBS orientation to a model that predicts expression from sequence we improve performance by 7.7%. Collectively, our results show that TFBS orientation and order have a significant effect on gene regulatory activity and need to be considered when analyzing the functional effect of variants on the activity of these sequences.

Gender Affirming Surgery in Nonbinary Patients: A Single Institutional Experience.

Background An increasing number of nonbinary patients are receiving gender-affirming procedures due to improved access to care. However, the preferred treatments for nonbinary patients are underdescribed. The purpose of this study was to investigate the goals and treatments of nonbinary patients. Methods A retrospective study of patients who self-identified as nonbinary from our institutional Gender Health Program was conducted. Patient demographics, clinical characteristics, surgical goals, and operative variables were analyzed. Results Of the 375 patients with gender dysphoria, 67 (18%) were nonbinary. Over half of the nonbinary patients were assigned male at birth ( n = 57, 85%) and nearly half preferred the gender pronoun they/them/theirs ( n = 33, 49%). A total of 44 patients (66%) received hormone therapy for an average of 2.5 ± 3.6 years, primarily estrogen ( n = 39). Most patients ( n = 46, 69%) received or are interested in gender-affirming surgery, of which, almost half were previously on hormone therapy ( n = 32, 48%). The most common surgeries completed or desired were facial feminization surgery ( n = 15, 22%), vaginoplasty ( n = 15, 22%), mastectomy ( n = 11, 16%), and orchiectomy ( n = 9, 13%). Nonbinary patients who were assigned male at birth (NB-AMAB) were more often treated with hormones compared to nonbinary patients assigned female at birth (NB-AFAB) (72% vs. 30%, p = 0.010). Conversely, patients who were AFAB were more likely to complete or desire surgical intervention than those who were AMAB (100% vs. 63.0%, p < 0.021). Conclusion Majority of nonbinary patients were assigned male at birth. NB-AFAB patients all underwent surgical treatment, whereas NB-AMAB patients were predominantly treated with hormone therapy.

Effect of Gender-affirming Facial Feminization Surgery on Psychosocial Outcomes.

OBJECTIVE: This study investigates the effect of gender-affirming facial feminization surgery (FFS) on psychosocial outcomes in patients with gender dysphoria. BACKGROUND: Comprehensive analyses of psychosocial outcomes after gender-affirming FFS are absent in the literature resulting in a paucity of information on the impact of FFS on quality of life as well as ramifications in health insurance coverage of FFS. METHODS: Scores from 11 validated, quantitative instruments from the Patient-Reported Outcomes Measurement Information System (PROMIS) assessing anxiety, anger, depression, global mental health, global physical health, satisfaction with sex life, positive affect, emotional support, social isolation, companionship, and meaning and purpose. Patients within the preoperative group (pre-FFS) were evaluated >30 days before surgery and patients within the postoperative group (post-FFS) were evaluated ≥10 weeks after surgery. RESULTS: A total of 169 patients [mean (SD) age, 33.5 (10.8) years] were included. Compared with the pre-FFS group (n=107), the post-FFS group (n=62) reported improved scores anxiety (56.8±8.8 vs 60.1±7.9, P =0.01), anger (47.4±7.6 vs 51.2±9.6, P =0.01), depression (52.2±9.2 vs 57.0±8.9, P =0.001), positive affect (46.6±8.9 vs 42.9±8.7, P =0.01), meaning and purpose (49.9±10.7 vs 46.2±10.5, P =0.03), global mental health (46.7±7.6 vs 43.1±9.2, P =0.01), and social isolation (52.2±7.5 vs 55.4±7.4, P =0.01). Multivariable analysis to account for the effects of other gender-affirming surgeries, hormone therapy duration, preexisting mental health diagnoses, socioeconomic disparities, and patient-reported quality of social relationships on psychosocial functioning demonstrated that completion of FFS was independently predictive of improved scores. CONCLUSIONS: Gender-affirming FFS improves the quality of life by multiple psychosocial domains in transfeminine patients.

Electrochemical Flux Synthesis of Type-I Na8Si46 Clathrates: Particle Size Control Using a Solid or Molten Na-Sn Mass Transport Mediator.

Sodium-filled silicon clathrates have a host of interesting properties for thermoelectric, photovoltaic, and battery applications. However, the metastability of the clathrates has made it difficult to synthesize them with the desired morphology and crystallite size. Herein, we demonstrate an electrochemical method whereby Na4Si4 dissolved in a Sn-based flux is converted to the Na8Si46 type-I clathrate using galvanostatic (constant current) oxidation. The temperature has a large influence on the products, with the reactions at 485 °C resulting in clathrates with small particle sizes (1-2 µm), while larger single crystals are obtained at 538 °C. The difference in microstructure is attributed to the solid vs liquid state of the Na-Sn phase at the reaction temperature, which is supported by the observed voltage profiles. The demonstrated method is promising for the tunable growth of Si clathrates and could be applicable to a broad range of intermetallic compounds.

Osteoprotegerin-eluting nanoparticulate mineralized collagen scaffolds improve skull regeneration.

Custom synthesis of extracellular matrix (ECM)-inspired materials for condition-specific reconstruction has emerged as a potentially translatable regenerative strategy. In skull defect reconstruction, nanoparticulate mineralized collagen glycosaminoglycan scaffolds (MC-GAG) have demonstrated osteogenic and anti-osteoclastogenic properties, culminating in the ability to partially heal in vivo skull defects without the addition of exogenous growth factors or progenitor cell loading. In an effort to reduce catabolism during early skull regeneration, we fabricated a composite material (MCGO) of MC-GAG and recombinant osteoprotegerin (OPG), an endogenous anti-osteoclastogenic decoy receptor. In the presence of differentiating osteoprogenitors, MCGO demonstrated an additive effect with endogenous OPG limited to the first 14 days of culture with total eluted and scaffold-bound OPG exceeding that of MC-GAG. Functionally, MCGO exhibited similar osteogenic properties as MC-GAG, however, MCGO significantly reduced maturation and resorptive activities of primary human osteoclasts. In a rabbit skull defect model, MCGO scaffold-reconstructed defects displayed higher mineralization as well as increased hardness and microfracture resistance compared to non-OPG functionalized MC-GAG scaffolds. The current work suggests that MCGO is a development in the goal of reaching a materials-based strategy for skull regeneration.

High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation.

The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary structures. The roles of DNA and RNA secondary structures in transcriptional regulation remain incompletely understood. However, advances in high-throughput assays have enabled genome wide characterization of some secondary structures. Here, we describe their regulatory functions in promoters and 3'UTRs, providing insights into key mechanisms through which they regulate gene expression. We discuss their implication in human disease, and how advances in molecular technologies and emerging high-throughput experimental methods could provide additional insights.

Synthesis of Type II Ge and Ge-Si Alloyed Clathrates Using Solid-State Electrochemical Oxidation of Zintl Phase Precursors.

Germanium clathrates with the type II structure are open-framework materials that show promise for various applications, but the difficulty of achieving phase-pure products via traditional synthesis routes has hindered their development. Herein, we demonstrate the synthesis of type II Ge clathrates in a two-electrode electrochemical cell using Na4Ge4-ySiy (y = 0, 1) Zintl phase precursors as the working electrode, Na metal as the counter/reference electrode, and Na-ion conducting ß″-alumina as the solid electrolyte. The galvanostatic oxidation of Na4Ge4 resulted in voltage plateaus around 0.34-0.40 V vs Na/Na+ with the formation of different products depending on the reaction temperature. When using Na4Ge3Si as a precursor, nearly phase-pure, alloyed type II Ge-Si clathrate was obtained at 350 °C. The Na atoms in the large (Ge,Si)28 cages of the clathrate occupied off-centered positions according to Rietveld refinement and density functional theory calculations. The results indicate that electrochemical oxidation of Zintl phase precursors is a promising pathway for synthesizing Ge clathrates with type II structure and that Si alloying of the Zintl phase precursor can promote selective clathrate product formation over other phases.