Our Work

Added #908 - Add nf-test snapshot for test_single_end profile (by @dialvarezs) #1028 - Add nf-test snapshot for test_longread_alternatives profile (by @dialvarezs) #1029 - Add nf-test snapshot for te…

Added #908 - Add nf-test snapshot for test_single_end profile (by @dialvarezs) #1028 - Add nf-test snapshot for test_longread_alternatives profile (by @dialvarezs) #1029 - Add nf-test snapshot for test_hybrid profile (by @dialvarezs) #1037 - Complement usage documentation with guidance on pipeline defaults, choices and alternatives (by @d4straub and @jfy133 ) #1039 - Add nf-test snapshot for test_longread profile (started by @brovolia, finished by @dialvarezs) #1041 - Refined and corrected unclear section of metromap (by @jfy133) #1042 - Add nf-test snapshot for test_default profile (by @dialvarezs) #1044 - Add new --gtdbtk_place_species parameter (by @dialvarezs) #1047 - Add --gtdbtk_single_job to run GTDB-Tk classification for all bins in a single job (requested by @sarah-shah-bioinf, by @dialvarezs) #1048 - Add optional PyPOLCA polishing for long-read assemblies via --run_pypolca (by @Harshita-sriv) #1055 - Add dedicated page describing resource usage (by @jfy133) #1057 - Add skip_fastqc switch (by @jorondo1) #1059 - Add --filtlong_filtering_by_shortreads parameter to enable filtlong's short-read-based long read filtering (by @dialvarezs) #1062 - Add --bin_seqkit_stats_max_forks parameter to cap concurrent bin-stats jobs (by @dialvarezs) #1063 - Add new --ale_per_base_output parameter to enable ALE per-base output (by @dialvarezs) Changed #1011 - Reverted CheckM2 database download workaround from #966 (by @dialvarezs) #1020 - Update CONCOCT subworkflow and modules (by @dialvarezs) #1030 - Updated to nf-core 4.0.2 template (by @dialvarezs) #1044 - Updated GTDB-Tk to v2.7.2 / GTDB r232 (by @dialvarezs) #1059 - Changed the default long read filtering tool from filtlong to chopper (by @dialvarezs) #1060 - Updated module tags to make them more specific (by @dialvarezs) #1061, #1064 - Speed up binning by not waiting for all mapping jobs to finish before starting (by @dialvarezs) #1062 - Remove grouping to prevent bin QC blocking by waiting for all binners (by @dialvarezs) #1063 - Run ALE with --metagenome and disable its per-base output by default (by @dialvarezs) #1065 - Improved efficiency by removing usage of per-bin GUNZIP module for bins and unbinned contigs and allowing gzip support for all modules (by @dialvarezs) #1066 - Improved efficiency by removing channel "locks" on Seqkit, QUAST, and GTDB-Tk (by @dialvarezs) #1070 - Update BUSCO nf-core module (by @dialvarezs) #1071 - Improved efficiency by batching DASTOOL_FASTATOCONTIG2BIN per binner instead of per bin (by @dialvarezs) #1074 - Exclude BUSCO output directories to reduce storage usage in output dir (by @dialvarezs) #1075 - Update output documentation to reflect BUSCO complete directory no longer being published (by @dialvarezs) #1079 - Add exit code 247 to the MEGAHIT retry error strategy (by @dialvarezs) #1080 - Updated to nf-core 4.0.3 TEMPLATE (by @dialvarezs) #1081 - Use subset database for geNomad (by @dialvarezs) #1084 - Disable NanoPlot static plot image files by default, since it depends on Chrome installed (by @dialvarezs) #1088 - Update Prokka (to v1.15.6), Prodigal and PyDamage modules, fixing conda/container output mismatches (by @dialvarezs) #1088 - Run GTDB-Tk with a single CPU on the test_single_end profile, so its outputs no longer depend on the machine running the test (by @dialvarezs) #1091 - Optimize process resource configs (by @dialvarezs) Fixed #1011 - Fix issue making CheckM2 running only for one sample per run (by @dialvarezs) #1012 - Prevent adapter trimming with Porechop on PacBio reads (by @dialvarezs) #1016 - Merge input reads on assembly input to prevent repeated filenames on multi-run samples (reported by @erikrikarddaniel, fix by @dialvarezs) #1017 - Prevent ALE running on long read assemblies when a sample has both LR and SR data (reported by @jfy133, fix by @dialvarezs) #1018 - Ignore catpack/summarise errors, since it's a limitation from the tool (reported by @jfy133, fix by @dialvarezs) #1018 - Feed catpack/contig with merged unbinned output to prevent execution errors (reported by @Juassis, fix by @dialvarezs) #1021 - Prevent execution of gtdbtk/summary when no bins pass QC (reported by @jfy133, fix by @dialvarezs) #1031 - Fix hybrid co-assembly with SPAdes (short & long reads with --coassemble_group) (fix by @d4straub) #1049 - Fix publishing issue with gtdbtk/classifywf (by @dialvarezs) #1058 - Make create_metabinner_bins.py save gzipped bin files to prevent NFS race condition (by @dialvarezs) #1069 - Exclude eukaryotic bins from CheckM2, which only supports bacterial and archaeal genomes (by @dialvarezs) #1076 - Add missing PyPOLCA citations to README, CITATIONS.md and the pipeline citation/bibliography text (by @dialvarezs) #1078 - Sort bins before GTDB-Tk classification so order-sensitive outputs are reproducible across environments (by @dialvarezs) #1084 - Update Prokka nf-core module, which pins GNU parallel to fix Prokka failures with Conda (by @dialvarezs) #1086 - Rename MaxBin2 bins inside the MAXBIN2 module via a patch instead of the ADJUST_MAXBIN2_EXT local module, which emitted dangling symlinks rather than bin contents on remote filesystems (by @dialvarezs) #1086 - Copy instead of move staged bins in TIARA_CLASSIFY, which emitted dangling symlinks rather than bin contents on remote filesystems (by @dialvarezs) #1086 - Match bin filenames exactly in TIARA_CLASSIFY so that e.g. bin .1 no longer also picks up bin .10 (by @dialvarezs) #1087 - Use non-mutating toSorted instead of in-place sort on shared channel items, which could cause ConcurrentModificationException failures (by @dialvarezs) #1093 - Ignore CheckM storage/ subdirectories in nf-test snapshots, whose contents vary between runs and machines (by @dialvarezs) #1094 - Convert depths in a single streaming pass, so CONVERT_DEPTHS no longer writes a decompressed copy of the depth file to the work directory and re-reads it once per read set, which stalled short-read assemblies for hours on object-backed work directories (by @dialvarezs) Dependencies | Tool | Previous version | New version | | --------------- | ---------------- | ----------- | | BUSCO | 6.0.0 | 6.1.0 | | GTDB (database) | r226 | r232 | | GTDB-Tk | 2.5.2 | 2.7.2 | | MultiQC | 1.31 | 1.34 | | Nextflow | 25.10.4 | 26.04.0 | | nf-core | 3.5.1 | 4.0.3 | | nf-schema | 2.5.1 | 2.7.2 | | Prokka | 1.14.6 | 1.15.6 | | pypolca | | 0.4.0 | Deprecated #908 - Removed local quast_bins_summary in favor of csvtk/concat (by @dialvarezs) #1018 - Remove mag_depths_plot local module (by @dialvarezs) #1018 - Deprecated --gtdbtk_skip_aniscreen in favor of --gtdbtk_place_species (by @dialvarezs) #1067 - Deprecated --skip_metaeuk as it has no effect, MetaEuk is gated by --metaeuk_db / --metaeuk_mmseqs_db (by @dialvarezs) #1086 - Removed adjust_maxbin2_ext local module, replaced by a patch on the MAXBIN2 nf-core module (by @dialvarezs) Full Changelog: https://github.com/nf-core/mag/compare/5.4.2...5.5.0

⚠️ Deprecations Deprecate casts from Categorical to integer dtypes (#28525) Deprecate not setting the plan_stage argument in show_graph() (#28391) 🚀 Performance improvements Pushdown len() to conca…

⚠️ Deprecations Deprecate casts from Categorical to integer dtypes (#28525) Deprecate not setting the plan_stage argument in show_graph() (#28391) 🚀 Performance improvements Pushdown len() to concat/union inputs (#28570) ✨ Enhancements Issue FutureWarning on using from_arrow of ArrowStreamExportable (#28442) Add infer_schema_files parameter to scan_csv (#28440) 🐞 Bug fixes Properly propagate enum metadata for iceberg column mapping (#28580) Correctly write parquet field IDs for enums and categoricals (#28581) Fix arrow C interop binview offset (#28623) Fix duplicate hive values in hive pre-partition rewrite (#28621) Double-counted offset for Arrow export of sliced Series(Array) (#28602) Struct/List/Array equality handling in sort and join (#28601) More careful slice pushdown into joins (#28578) Preserve ordering in sliced unions (#28576) Drop input sortedness when casting to a string (#28574) Clear sortedness flags in StringChunked substring kernels (#28573) Bad mask handling when reading optional parquet column (#28547) Any operation on Unknown(Int) and Unknown(Float) should result in Unknown(Float) (#28545) Flip nulls_last after Expr.reverse() (#28572) Fix high blocking thread use in sink_parquet with async local path (#28543) Serialize LazyFrames backed by bytes (#28568) Release GIL in SQLContext.execute() (#28549) Propagate nulls_last in function_expr_sortedness (#28544) Incorrect slicing when a join requires sorting (#28541) 🛠️ Other improvements Fix duckdb delta extension install collision (#28607) Thank you to all our contributors for making this release possible! @BitWeaverDev, @Matt711, @Samoilov2004, @borchero, @dancsi, @dsprenkels, @kdn36, @masumi-ryugo, @nameexhaustion and @ritchie46

In India, female infertility constitutes a major public health problem, affecting millions of women who reside within diverse socio-economic, socio-cultural, and geographical environments. The current…

In India, female infertility constitutes a major public health problem, affecting millions of women who reside within diverse socio-economic, socio-cultural, and geographical environments. The current study reviews data available in the literature regarding epidemiology of female infertility in India, including prevalence, aetiology, incidence trends, and geographic variations. Rates of primary infertility range from 3.9% to 16.8%, depending upon the region in question, with secondary infertility making up a significant proportion of all infertile cases. Some of the main determinants of infertility among Indian females include polycystic ovary syndrome (PCOS), reproductive tract infection, tuberculosis, undernourishment, early marriages, delayed first pregnancy, and more recently developed causes, such as obesity. There is an observable variation in prevalence rate with respect to different geographic regions, being high among eastern and northeastern states of India due to their poverty levels, less medical care accessibility, and a higher burden of infectious diseases. Urban areas have been increasingly reporting cases of infertility related to delayed pregnancies and lifestyle issues, while those residing in rural areas are mainly affected by infectious causes and undernourishment. This review highlights the urgent need for region-specific, integrated public health interventions, improved surveillance systems, and equitable, culturally sensitive reproductive healthcare services to address the complex and evolving burden of female infertility in India.

In this paper, modified version of the Fast Haar Transform algorithm is developed, and its impact on computational efficiency and memory requirements is analyzed. Unlike the traditional Fast Haar Tran…

In this paper, modified version of the Fast Haar Transform algorithm is developed, and its impact on computational efficiency and memory requirements is analyzed. Unlike the traditional Fast Haar Transform algorithm, which performs calculations based on two-node structures, the improved algorithm utilizes four-node structures simultaneously to determine spectral coefficients. This enhanced approach reduces the number of iterations, optimizes redundant computations, and minimizes memory consumption. The modified Fast Haar Transform algorithm is represented in both graph-based and matrix-based forms, and a comparative analysis with the conventional Fast Haar Transform is provided.

Human aging is a complex biological process characterized by interconnected molecular, cellular, tissue, and organ-level alterations resulting from the interactions of genetic, epigenetic, biochemical…

Human aging is a complex biological process characterized by interconnected molecular, cellular, tissue, and organ-level alterations resulting from the interactions of genetic, epigenetic, biochemical, and morphological mechanisms. In recent years, increasing attention has been directed toward understanding aging as a multilevel integrated system rather than evaluating it through individual biomarkers. The aim of this study is to comprehensively analyze human aging from the perspectives of molecular biology, oxidative stress, histology, and gross anatomy, and to integrate these disciplines into a unified micro–macro conceptual framework. The study examines the roles of telomere shortening, DNA damage, epigenetic modifications, cellular senescence, mitochondrial dysfunction, and oxidative stress in the mechanisms underlying aging based on contemporary scientific evidence. Furthermore, the relationship between histological alterations observed in the skin, skeletal muscle, bone, liver, kidney, and brain tissues and their corresponding macroscopic anatomical manifestations is discussed. Based on this analysis, an integrated micro–macro aging model is proposed, illustrating a continuous biological cascade from molecular alterations through cellular and tissue remodeling to progressive organ dysfunction and the development of clinical manifestations of aging. This model provides a comprehensive framework for identifying aging biomarkers, improving the assessment of biological age, facilitating the early diagnosis of age-related diseases, and supporting the development of personalized preventive and therapeutic strategies. The findings of this study offer both theoretical and practical contributions to future research in gerontology, molecular biology, histology, anatomy, and regenerative medicine.

This paper compares two deep-learning models for recognizing plant diseases from leaf images: the EfficientNet-B0 classifier and the YOLOv11 detector, both tested on the PlantVillage dataset. Instead …

This paper compares two deep-learning models for recognizing plant diseases from leaf images: the EfficientNet-B0 classifier and the YOLOv11 detector, both tested on the PlantVillage dataset. Instead of only reporting accuracy numbers, we show the mathematics behind them. We write out the main formulas each model uses — image normalization, the depthwise-separable convolution, the SiLU activation, softmax cross-entropy, intersection-over-union, and the CIoU, distribution-focal, and cross-entropy losses of the detector — and then work through the numbers by hand. For example, one 3×3 layer is shown to need 6.55 times fewer operations when depthwise separation is used, a cross-entropy of 0.417 is computed for a sample output, an intersection-over-union of 0.681 gives a CIoU loss of 0.328, and a distribution-focal loss of 0.773 is found. We also rebuild the precision, recall, and F1 scores from confusion counts (for one class: precision 99.0%, recall 98.0%, F1 98.5%), compute an average precision of 0.943, and run a paired t-test that gives t(4)=5.62, p≈0.005. EfficientNet-B0 reaches 98.5% accuracy with 5.3 M parameters and 0.39 GMACs, while YOLOv11 reaches 97.8% accuracy and a mAP@0.5 of 96.2% but needs about 55 times more computation. The classifier is faster and slightly more accurate, while the detector is more expensive but also locates the disease.

Polarization mismatch between transmitting (TX) and receiving (RX) antennas increases the polarization loss factor (PLF), leading to significant signal degradation in mobile communications. This issue…

Polarization mismatch between transmitting (TX) and receiving (RX) antennas increases the polarization loss factor (PLF), leading to significant signal degradation in mobile communications. This issue is particularly unavoidable for linear polarization (LP) when antennas are dynamically oriented. This paper investigates the design and operational mechanisms of polarization-compliant antennas that enable adaptive alignment. By employing an output-ratio tunable power divider to excite dual-polarized elements, the system can simultaneously alter polarization orientation. The divider utilizes a 90-degree hybrid directional coupler controlled by a phase shifter to achieve high-accuracy, high-resolution power division. The feasibility of this approach is demonstrated through conceptual implementations and numerical simulations, further validated by experimental measurements.

Mazkur tezisda COVID-19 pandemiyasidan keyingi davrda zamonaviy tibbiyot terminologiyasining shakllanishi va rivojlanishi xitoy, ingliz hamda o‘zbek tillari misolida qiyosiy tahlil qilinadi. Tad…

Mazkur tezisda COVID-19 pandemiyasidan keyingi davrda zamonaviy tibbiyot terminologiyasining shakllanishi va rivojlanishi xitoy, ingliz hamda o‘zbek tillari misolida qiyosiy tahlil qilinadi. Tadqiqotda pandemiya davrida keng qo‘llanilgan 新冠肺炎 (xīnguān fèiyán), 核酸检测 (hésuān jiǎncè), 健康码 (jiànkāngmǎ), 无症状感染者 (wú zhèngzhuàng gǎnrǎnzhě) kabi xitoycha hamda COVID-19, SARS-CoV-2, Long COVID, social distancing, self-isolation, contact tracing kabi inglizcha terminlarning shakllanishi, semantik xususiyatlari va yasalish modellari tahlil qilinadi. Shuningdek, ushbu terminlarning o‘zbek tiliga o‘zlashish jarayoni, ularning milliy terminologik tizimga moslashuvi hamda termin yasashning asosiy usullari qiyosiy jihatdan o‘rganiladi. Tadqiqot natijalari pandemiyadan keyingi davrda tibbiyot terminologiyasining boyishi, xalqaro terminlarning standartlashuvi hamda xitoy, ingliz va o‘zbek tillari o‘rtasidagi terminologik o‘zaro ta’sirning kuchayganligini ko‘rsatadi.

This archive contains sample data products generated by the H-Snow daily 10 m snow cover mapping framework, including the dataset and accompanying documentation. The dataset spans the period from 2002…

This archive contains sample data products generated by the H-Snow daily 10 m snow cover mapping framework, including the dataset and accompanying documentation. The dataset spans the period from 2002 to 2025, with data organized in folders corresponding to each calendar year. Daily data files are named following the yyyy_doy.tif convention, where doy denotes the day of the year.   Pixel values within each GeoTIFF range from 0 to 255: 0 represents no-data areas outside the watershed boundary, 85 indicates snow cover, 170 corresponds to snow-free land surfaces, and 255 denotes water pixels.   The original dataset has a spatial resolution of 10–20 m. Due to file size upload constraints, the distributed sample data has been resampled to 100 m and compressed. Nevertheless, the products retain substantial spatial detail and are suitable for qualitative analysis.

Coumarin is a naturally occurring phytochemical that exhibits various pharmacological activities, including anti-inflammatory, antioxidant, antimicrobial and wound-healing properties. However, its top…

Coumarin is a naturally occurring phytochemical that exhibits various pharmacological activities, including anti-inflammatory, antioxidant, antimicrobial and wound-healing properties. However, its topical therapeutic effectiveness is limited due to poor aqueous solubility and inadequate skin permeation. Transferosomes are highly deformable lipid vesicles capable of penetrating the stratum corneum and delivering drugs into deeper layers of the skin, thereby enhancing topical drug delivery. The present study aimed to formulate and evaluate a coumarin loaded transfersomal gel for improved topical delivery. Coumarin loaded transferosomes were prepared using the thin-film hydration method with phospholipids and an edge activator. The prepared vesicles were evaluated for vesicle size, polydispersity index, zeta potential and percentage drug content. The optimized transfersomal formulation was incorporated into a Carbopol gel base and further evaluated for appearance, pH, viscosity, spreadability, drug content, in vitro drug release and ex vivo skin permeation. The optimized transfersomal gel exhibited uniform appearance, suitable pH, good spreadability and sustained drug release with enhanced skin permeation compared to the plain coumarin gel. The findings suggest that the coumarin-loaded transfersomal gel is a promising topical drug delivery system capable of improving the therapeutic efficacy of coumarin by enhancing its skin penetration, prolonging drug release and increasing local drug availability. Therefore, transfersomal gel represents a potential carrier for the effective topical treatment of skin disorders.